I increased  nthethreads value in featureCounts but the running time didnt decrease.

I used the following command:
subread_res <- featureCounts(files, annot.ext = GTF_file,
                             isGTFAnnotationFile = TRUE, nthreads = X,
                             countMultiMappingReads = TRUE, fraction = TRUE)

First run with 5 threads, 2.7 min used

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           S /Result ... ||
||                                                                            ||
||      Dir for temp files : .                                                ||
||                 Threads : 5                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||         Strand specific : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file us_muscu ... ||
||    Features : 729264                                                       ||
||    Meta-features : 48795                                                   ||
||    Chromosomes/contigs : 45                                                ||
||                                                                            ||
|| Process BAM file sults/01_STAR_r ... ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 53383794                                                  ||
||    Successfully assigned reads : 12345398 (23.1%)                          ||
||    Running time : 2.70 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

then with 1 thread, 2.73 min. Nearly no difference. How are your data with the nthreads? Suggestions? Thanks!

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 1.26.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           S s/Result ... ||
||                                                                            ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||         Strand specific : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file ensembl_86/Mus_muscu ... ||
||    Features : 729264                                                       ||
||    Meta-features : 48795                                                   ||
||    Chromosomes/contigs : 45                                                ||
||                                                                            ||
|| Process BAM file Results/01_STAR_r ... ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 53383794                                                  ||
||    Successfully assigned reads : 12345398 (23.1%)                          ||
||    Running time : 2.73 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

Bellow is the session info

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: .linuxbrew/Cellar/r/3.4.1_2/lib/R/lib/libRblas.so
LAPACK: .linuxbrew/Cellar/r/3.4.1_2/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rsubread_1.26.1

loaded via a namespace (and not attached):
[1] compiler_3.4.1

First you will need to check if more than one CPU core was used when you ran with multiple threads. You can run 'top' command under linux shell to see how many cpu cores you are using.

Another possibility is that most of featureCounts running time was spent on reading in and decompressing your bam file and running with multi threads wouldn't help for this.