Chitosan (CS) metal complexes with bivalent metal ions, including Cu(II), Zn(II), Fe(II) were prepared, and characterized by FT-IR, XRD, AAS and elemental analysis. The crystalline and structural properties of chitosan-metal complexes were different from those of chitosan, and the -NH2, -OH groups in chitosan molecule were considered as the dominating reactive sites. In vitro antimicrobial activities of the obtained chitosan-metal complexes, which were found to be much better than free chitosan and metal salts, were examined against two gram-positive bacteria (S. aureus and S. epidermidis), two gram-negative bacteria (E. coli and P. aeruginosa) and two fungi (C. albicans and C. parapsilosis). Results indicatd that the inhibitory effects of chitosan-metal complexes were dependent on the property of metal ions, the molecular weight and degree of deacetylation of chitosan and environmental pH values. Electro microscopy confirmed that the exposure of S. auresus to the chitosan-Cu(II) complex resulted in the disruption of cell envelop. Based on the discussion upon the antimicrobial mechanism of chitosan-metal complexes and their molecular structures, the structure-activity correlation for the antimicrobial activities was elucidated. All the results show that chitosan-metal complexes are a promising candidate for novel antimicrobial agents that can be used in cosmetic, food, textile et al.