This paper proposes a new control strategy applied to a new input series output parallel (ISOP) DC/DC converter system. In the new ISOP system, an improved phase shifted full bridge soft switching topology is utilized. In the topology, clamping diodes and resonant inductors are used to realize soft switching of the main power switch and reduce the voltage spike of the secondary rectifier diodes. In order to achieve input voltage sharing (IVS), hysteresis compensation IVS control strategy is proposed based on common duty cycle control method. The new control strategy can achieve stable working for the system, improve IVS balancing accuracy, and simplify the design process of control system. This paper analyzes the working principle of the main circuit and control circuit. The small signal model of ISOP system is established and the controller design process is given. A 500 W prototype is designed to verify the effectiveness of the proposed converter and the control system.