In order to solve the problem of the micro flow cell clogging,and to improve the reliability of the flow cytometry system,a new method was proposed for hydrodynamic self-cleaning system.By analyzing the flow cell focus principle,we considered that to obtain stable single cell flow,the stable pressure in the flow chamber must be ensured.Therefore,we established a diagnosis method of clogging by the pressure detecting,and designed a self-cleaning system.Then we built up corresponding experimental systems.Experiments and testing showed that the selfcleaning system could improve the flow and resolve the clogging problem.