Abstract: Using the technique of Particle-In-Cell to simulate the secondary electron effect of proton beams bombarding the target surface, we obtained the results of the quality of proton beams and the quantity of secondary electrons affected by the extracted voltage. From which, we find that the width of proton beams' waist is 1.8 mm at 50 kV and 1.2 mm at 150 kV. Therefore, the proton beams become dispersed at lower voltages and compact at higher voltages. Adjusting the extracted voltage between acceleration areas, we can control the quality of proton beams.