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 self-cleaning system could improve the flow and resolve the clogging problem.