A self-developed hydrodynamic cavitation generator with triangular multi-orifice plates in the Hydraulics Laboratory at Zhejiang University of Technology was used to sterilize raw water in Shengli River of Hangzhou. Pressure in hydrodynamic cavitation working section were measured by the pressure data acquisition system. Morphological changes in coliform were observed by the biological microscope. Total colony count was detected by plate counting method, and enzyme substrate technique was used to detect total coliform and Escherichia coli. Effects of cavitation number, different initial concentration of raw water, number of orifice, size of orifice and arrangement of orifice on killing pathogenic microorganisms by hydrodynamic cavitation were experimentally studied. Choosing the appropriate initial concentration, increasing the orifice number, decreasing the orifice size and improving orifice arrangement could further increase the killing rates of pathogenic microorganism in raw water. The killing rate of the bacteria colony can reach stable and efficient killing value at 5min. At 15min the killing rate of total colony count reached 80%, and more than 90%, even 100% total coliform and Escherichia coli were killed.