To understand the amino acid compositions of the muscles and the calipashes in Chinese soft-shell turtle(Pelodiscus sinensis), and to comprehensively evaluate their nutritional value, we collected muscles and calipashes from 6 P. sinensis(3 males and 3 females) with an average weight of (1000±50) g during the three periods of pre-hibernation, mid-hibernation and post-hibernation. The results showed as follows: 17 amino acids were contained in both muscles and calipashes during the three periods of pre-hibernation, mid-hibernation and post-hibernation, where the mass fraction of glutamic acid was the highest in the muscles while it was glycine with the highest mass fraction in the calipashes, and the mass fractions of total 17 amino acids(TAA) in P. sinensis muscles during the pre-hibernation period(M1) was significantly higher than ones during the mid-hibernation period(M2) and post-hibernation period(M3)(P<0.05), however, those in the calipashes were significantly higher during both pre-hibernation period(S1) and mid-hibernation period(S2) than during post-hibernation period(S3)(P<0.05). Among the essential amino acids, the mass fraction of lysine was the highest in the muscles and the ratios of the mass fraction of essential amino acids(EAA) to TAA and EAA to total non-essential amino acids(NEAA) were significantly higher in the muscles than in the calipashes(P<0.05), which were also higher in the muscles than in the ideal FAO/WHO protein recommendations(40% and 60%). The mass fractions of total delicious amino acids(DAA) and the ratios of DAA/TAA were significantly lower in the muscles than in the calipashes(P<0.05). The results of amino acid score(AAS) and chemical score(RC) among evaluating 9 essential amino acids showed that except valine(Val) of muscle during M2, the AAS and RC of the methionine and cystine(Met+Cys) sum in the rest of the groups were the lowest ones, and their differences were statistically significant in the muscles and in the calipashes(P<0.05), the chemical score of Met+Cys was also the lowest one in the muscles and in the calipashes of all groups, which indicated that Val was the first restricted amino acid component of the muscles during M2, and Met+Cys was the one of both the muscles and the calipashes during the other two periods, and the balance peculiarities of amino acids in the muscles were superior to ones in the calipashes. The results of essential amino acid index(EAAI) higher than 70 indicated that the quality of muscle protein was a high quality protein source. There were significantly higher in the muscles than in the calipashes for EAAI, biological value and nutrition index in P. sinensis(P<0.05). The orders of the amino acids grey correlation(GC) in P. sinensis showed that GC in the muscles during M2 was the lowest one among three periods, while its in calipashes during S2 was the highest one, which were significantly higher in the muscles than in calipashes(P<0.05), which meant the balance of amino acids in P. sinensis of the muscles during M2 was inferior to the ones during M1 and M3, and its in the calipashes was inferior to the one in the muscles. The results of clustering tree analysis also showed that the amino acid proportions of the muscles were more reasonable than ones in the calipashes which revealed that the qualities of amino acids in the muscles were better than those in the calipashes.