The invention aims to develop a flow-cytometry-based method for rapidly measuring heterotrophic bacteria in a eutrophic lake. The method is a flow-cytometry-based bacterium counting method. The method comprises the following steps of fixing a sample, performing ultrasonic processing, filtering, performing SYBR Green I dyeing, detecting the heterotrophic bacteria by utilizing a flow cytometer, and acquiring forward and lateral scattering light, an SYBR Green I green fluorescence signal and a chlorophyll a red fluorescence signal of autotrophic plankton, wherein the SYBR Green I green fluorescence signal is used for setting a threshold value; and eliminating the influence of the nannoplankton on bacterium detection by utilizing the forward and lateral scattering light, separating the plankton from abiological particles and cellular debris according to the intensity of the SYBR Green I green fluorescence signal, and separating the bacteria from phytoplankton according to the intensity of the chlorophyll a red fluorescence signal of the autotrophic plankton, thereby obtaining the accurate number of the heterotrophic bacteria. The method has the time-saving and labor-saving effects, the large-scale ecological survey can be developed, and the counting precision and accuracy of the bacteria are improved.