Rhesus macaque (Macaca mulatta) is the most extensively studied nonhuman primate species for human biomedical modeling. However, little is known about the biological pattern of genome-wide structural variations (SVs) and the evolutionary forces underlying SVs in this species. Here, we conducted genomic sequencing and analyses based on Nanopore long-reads and Illumina short-reads technologies. We called SVs between the two subspecies (China vs. India), using three methods of assembly-based and long-reads-based algorithms. Interestingly, we found significantly more SVs in the X-chromosome than in autosomes, consistent with the expectation of the faster-X divergence at the subspecies level. With the fine-scale methylation frequencies and recombination rates, we found duplications with significantly lower methylation frequencies while higher recombination rates than other types of SVs, suggesting a higher level of transcriptional and evolutionary potential for duplications than for other SVs types. A genome-wide scan of selective sweeps revealed that over 3% of SVs are under positive selection and that X chromosome showed significantly higher number of positively selected SVs than do autosomes, suggesting the “faster-X effect” of SVs. Thus, our study revealed a different evolutionary importance of duplications compared with other SVs forms in producing raw material upon which selective forces, including the faster-X effect, can further play.