The pulse load of an integrated power system (IPS) ship can produce very high power intermittently in a short period of time. Owing to the limited DC bus capacitance, the periodic pulse load charging and discharging process can make the IPS system state variables have a periodic alternating process during electromagnetic transients, especially at the bus voltage. In order to alleviate this problem, it is necessary to find a suitable control strategy. At first, this article establishes a mathematical model of DC bus voltage dynamics and propulsion motor load. Then, a flexible energy scheduling algorithm is proposed to coordinate the propulsion motor load and the pulse load based on the flexibility of IPS energy scheduling and the concept of virtual inertia. This algorithm can adaptively change the virtual inertia of the DC bus according to the pulse load power level and the propulsion motor load level to mitigate the impact of the pulse load on the IPS system. At the same time, the algorithm is also distributed and has little impact on the propulsion system. Finally, the effectiveness of the algorithm is verified through the mixed simulation of PSCAD and MATLAB and the hardware in the loop test.