Abstract: In the experiment research of the pulse ion beam using small mass analysis system, the pulse beam is extracted from vacuum arc ion source with high beam current pulse amplitude and low energy. The space charge effect can make beam diverge rapidly, and this will result in large uncertainty in the analysis of hydrogen ion beam composition. In order to overcome the difficulty to focus pulse ion beam in narrow interspace range, a new ion beam focusing device with double limit beam diaphragm and three-flakelet electrostatic lens was developed. The double limit beam diaphragm is mainly used to reduce beam divergence. The three-flakelet electrostatic lens is very fit for pulse ion beam focusing in small size vessel. The computer procedure simulation was in accord with the design idea for focusing the high pulse ion beam. Using this focusing device in magnet mass spectrograph, ion beam current pulse amplitude to diverge into analysis box of the mass analyzer is reduced to 0.06 mA. The uncertainty of pulse ion beam mass analysis decreases.