I'm using Gviz package to show ChIP-Seq signals on specific sites. These signals were represented as polygon with y-axis ticks automatically set by Gviz. It seems the only controllable parameters are ylim, which set the min and max of DataTrack, while there are no options like "breaks" to exactly control the position and amounts of ticks. Is there any solution for this issue?

You could play around with the cex.axis parameter to control the axis annotation font size. This is currently driving the calculation of axis ticks. There is no direct way to define the number of ticks or similar. Sorry.

Florian