Objectives： In order to investigate the mechanism of different inhibitory effects of chitosan on some microorganisms. Methods： The minimum inhibitory concentration （MIC） and minimum bactericidal concentration （MBC） of chitosan were determined， and the relative conductivity， dissolved OD260nm value， dehydrogenase and β-galactosidase activity were measured. Results： The results showed that the MIC of chitosan to Lactobacillus plantarum， Escherichia coli and Saccharomyces ellipsoideus were 0.2， 2， 0.4 mg/L， MBC were 0.8， 16 mg/L and 3.2 mg/L， respectively. 4MIC chitosan significantly increased the relative conductivity and OD260nm value of all microorganisms. MIC chitosan treatments increased the relative conductivity of all microorganisms and OD260nm value of S. ellipsoideus significantly， but the OD260nm value of E. coli decreased， and no significant difference was found in L. plantarum at 0.5 h， but its increased significantly at 9 h. Chitosan significantly inhibited the dehydrogenase of L. plantarum and S. ellipsoideus， but had no significant effect on E. coli. The inhibition effect of chitosan on β- galactosidase was weaker than that of dehydrogenase. Conclusions： Chitosan was easy to pass through the cell wall of L. plantarum and S. ellipsoideus， also damage cell membrane of S. ellipsoideus. But it was difficult to pass through E. coli cell wall. The difference of antibacterial activity of chitosan might be related to the barrier ability of cell wall and resisting destruction of cell membrane to chitosan.