Beam illumination system is an important part of flow cytometry,and the key for rapid and accurate cell detection. A single-cell illumination system for the flow cytometry based on cylindrical lens is proposed,and its principle is further studied using geometrical optics and physical optics respectively. The intensity distribution expression of the illumination beam is deduced,and the system is simulated and optimized by ZEMAX and MATLAB software respectively. Based on this,the illumination intensity distribution is tested. The theoretical analysis and experimental results indicate the feasibility and effectiveness of the scheme.