Abstract: 【Objective】 To screen SNP polymorphisms in PPARγ, MYF5and AGPAT5 closely related to the regulation of muscle growth and development, lipid metabolism and meat quality, and reveal the effects of SNP mutations on body size traits in Xinjiang brown cattle. 【Methods】 The mutation of gene PPARγ, MYF5 and AGPAT5 in Xinjiang brown cattle were screened by PCR-RFLP method.The haplotype blocks of the above three target genes were constructed by haplotype method, and the genotype frequencies of different haplotypes were counted. 【Results】 SNP association analysis showed that six SNP loci of the three genes had structure PPARγ- Exon7 (g74t) and AGPAT5-exon7 (g72a) led to changes in mRNA secondary structure and free energy, and protein secondary structure prediction revealed that two SNPs in both exon 1 of PPARγand exon 7 of AGPAT5 were missense mutations, which could change amino acid, but no impact on protein secondary structure. 【Conclusion】 In this study, six polymorphisms in PPARγ, MYF5, and AGPAT5 genes were screened, and through genotyping, association analysis and bioinformatics analysis, and marker AGPAT5, PPARγ, MYF5 and AGPAT5 determined the relationship with body size traits by information for molecular breeding of Xinjiang brown cattle.