A self-developed Venturi-type hydrodynamic cavitation reaction device was used. Escherichia coli was selected as the indicative bacterium of pathogenic microorganism, and water samples containing E. coli were sterilized. Killing rates of E. coli were detected by agar plate counting method. Morphological changes in E. coli before and after cavitation were observed with a biological microscope. The effects of varying throat lengths, initial concentration, throat velocity, treatment time and cavitation number on the killing rates of E. coli were analyzed. The experimental results showed that the killing effect of E. coli was best at relative throat length L/R=60. Also, lowering cavitation number, increasing throat velocity, prolonging treatment time, and choosing a suitable initial concentration of E. coli can be helpful to improving the killing rates of E. coli.