Abstract: In this papert the influence of molecular structure of protein on the acoustic nonlinearity parameter B/A has been studied.By using biochemical technique,three proteins (bovine serum albumin,bovine hemoglobin,pepsin) were employed and their secondary,tertiary and quarternary protein structures were perturbed by the denaturing agent sodium dodecyl sulfate (SDS) solution,while their primary structures of protein were not changed.This means that only the structural features were altered and the chemical composition maintained unchanged.B/A have been measured by using improved thermodynamic method.The experimental results show that when the concentration of SDS solution increases,the alterations of the protein structure increase,and the contribution of protein to the B/A values decreases.Results indicate that the B/A values can display the destruction of molecular structure of protein.Some explanation of these phenomena has also been made in this paper.