Three wild populations of Protosalanx hyalocranius were sampled from nature waters of Lianhuanhu lake in Heilongjiang Province(HL), Taihu Lake in Jiangsu Province(JT) , Shitoukoumen Reservoir in Jilin Province (JS)respectively. The capture was conducted in December 2010. The muscle nutritional composition of P. hyalocraniuss from three different areas had measured by conventional biochemistry. As a result, crude protein and moisture content of fish from three areas had no significant difference (P >0.05) , while there was significant difference in crude fat content among the three populations (P<0.05) . Fish from JT had the highest total and nonessential amino acid contents (76.14%and 45.57%, dry weight) .The lowest total and nonessential amino acid contents were 71.54% and 42.64%, of fish from HL. There was significant difference of flavor acids in JS compared with that in other two populations (P<0.05). There was no significant difference of total fatty acid content among the three populations (P >0.05) . Fish from JT had higher essential amino acid index, amino acid score and chemical score than those of the other two populations. There was significant difference of total saturated and unsaturated fatty acid contents in HLcompared with that in other two populations (P<0.05). Based on the clustering analysis, it was apparent that the nutritional quality of fish from JT and JL was better than that from HL.