Abstract: In this paper,the quality of muscle in Schizothorax prenanti Tchang of different weight was analyzed and the Real-time PCR was applied to explore the relative expression of PGC-1α and PPARγ of the fish in different tissue. The results showed that the content of protein and crude fat in Schizothorax prenanti Tchang of different weight were significant difference(p<0.05). The content of moisture and ash were revealed to be no significant difference(p>0.05). The pH value in muscle was no difference. The dehydration rate in big fish was higher than the medium and small fish. The contents of total amino acids,essential amino acids and the umami amino acids in small and medium fish were higher than the big one. The quality of muscle in small and medium fish was better than big one. The relative expression of PPARγ in the head kidney,liver and muscle of Schizothorax prenanti fish of different qualities was existed significant difference(p<0.05). The relative expression of PGC-1α in the head kidney existed significant difference(p<0.05),and revealed no significant difference(p>0.05) in liver and muscle.The expression of PPARγ and PGC-1α had a certain correlation with the crude fat in muscle.