Smoke-cooked chicken sausage was used as carrier in this research in order to establish the method for measuring the secondary structure of protein.The effects of soybean protein isolate were measured for the changes of protein structure in smoke-cooked chicken sausage by Fourier transformation infrared spectroscopy (FT-IR) and the secondary structure of protein was quantitative analyzed by FT-IR in microstructure.The results showed that contents of α-helix and β-sheet were in downward trend obviously as a whole,which from 9.99% and 43.62% to 5.53% and 36.49% respectively.When soybean protein isolate was added to 10%,the irregular structure and β-tum were reached to the maximum value.The secondary structure of protein in chicken sausage was transformed from orderly structure to disorder with the increasing of soybean protein isolate.When added the appropriate soy protein isolate in samples,which can maintain the stability of secondary structure of protein and improve the edible quality of smoke-cooked chicken sausage.Therefore,FT-IR combined with computer-aided analysis is one of the effective methods for researching the secondary structure of protein.