The performance of multi-pulse position modulation inter-satellite optical communication system is analyzed. For the shot-limited system, the analytical expression of the average symbol error rate (ASER) is given. For the thermal-limited system, the analytical expression of tight upper bound on the ASER is derived. The validity of theoretical calculations is verified. The results of numerical simulations show that the system performance degrades with the increase of jitter variance, and for the different power regions, the performance of the system varies with the different beam waist radiuses. When the number of signal slots per symbol is constant, increasing the number of time slots per symbol will increase the system performance, but the bandwidth utilization reduces as well. Therefore, when selecting system parameters, the above factors need to be considered comprehensively.