[Objective] To study the photodynamic inactivation of Gram-positive bacteria Staphylococcus aureus and Gram-negative bacteria Escherichia coli by hematoporyrin monomethyl ether. [Methods] Bacteria incubated with different concentrations of hematoporyrin monomethyl ether (HMME) and then irradiated with visual light for 30minutes, bacteria inactivation efficiency was detected with the reduction of colony unit, and morphological changes were observed with atomic force microscope (AFM). [Results] Results indicated that 90% of Staphylococcus aureus was photoinactivated by illumination with visible light for 30 min (power density 200 mW/cm2) in the presence of 50 mg/mL HMME. The bacteria killing efficiency to Staphylococcus aureus with light irradiation was much obvious than that in dark at the same concentration of HMME, although without noticeable damage to E. coli with illumination or in dark. AFM ultrastructure images showed that the cells surface of photodynamic inactivated bacteria was all damaged seriously without the leakage of cell contents. [Conclusion] We concluded that the attacked sites to bacteria cells by hematoporyrin monomethyl ether were bacteria membrane structure. Atomic force microscopy provides us a visual technique to study the mechanism of bacteria reacted with photosensitizers.