Live baits Calanus sinicus were used to make an indoor experimental study on the intermediate and lower levels “phytoplankton-Calanus sinicus-anchovy (Engraulis japonicus)” in key species food chain of the Yellow Sea and East China Sea food web so as to know the transfer process of amino acids in the food chain. After making a cultural experiment for 76 days, the quantitative analysis of contents of 14 amino acids in the collected samples was made. It is shown from the analysis results that the copepod Calanus sinicus forms an intermediate key link, that is, the copepod not only transforms the vegetable protein of chlorella into animal protein of copepod and greatly raises the lysine content, but also raises the total amino acid content from 6.10% of chlorella to 24.16% of copepod. As an important bait of commercial fish in this food web, anchovy (Engraulis japonicus) further raises the total amino acid content of copepod to 27.06% of anchovy. There is a significant correlation between relative amino acid compositions of Calanus sinicus and chlorella (r=0.606, p<0.05), among them, the correlation between the percent contents of 7 essential amino acids of Calanus sinicus and chlorella was relatively poor, and that between the percent contents of 7 non-essential amino acids is relatively strong. The percent contents of amino acid of anchovy Engraulis japonicus changed with the change in baits when food of anchovy changed from synthetic bait to live Calanus sinicus. The amino acid contents of anchovy egesta are dependent mainly on metabolic process of anchovy.