This study investigated genomic structural variations and their association with muscle development in Qinghai-Tibetan Plateau yaks to elucidate their genetic diversity and adaptive mechanisms. Whole-genome resequencing was performed on 145 Qinghai-Tibetan Plateau yaks, supplemented with sequence data from 12 wild yaks obtained from the National Center for Biotechnology Information (NCBI) database. Analyses characterized runs of homozygosity (ROH), copy number variations (CNV), and structural variations (SV). A genome-wide copy number variation map for Qinghai Plateau yaks was constructed. Qinghai-Tibetan Plateau yaks exhibited numerous ROHs (totaling 61,074 segments, covering 19,947.56 Mb), showing relatively high levels of genomic homozygosity compared to wild yaks (3255 segments, 1056.66 total length), and 1175 CNV regions and 59,694 SVs, primarily located in non-coding regions, were identified. Publicly available transcriptome data were integrated to identify candidate genes related to muscle development, followed by statistical validation of key candidates. Integrating genomic and transcriptomic data revealed 84 overlapping genes potentially involved in muscle development. Subsequent bioinformatic prioritization identified PTPN6, ATP2A1, LCP1, GNA15, ALOX5AP, FLT3, SLC34A3, and BCL11A as high-priority candidate genes potentially influencing this trait. These findings demonstrate that genomic variations significantly impact muscle development in Qinghai-Tibetan Plateau yaks, providing a valuable molecular basis for future yak breeding programs and adaptation research.