Due to the extensive application of converter parallel system with multiple-energy storage converters in DC systems, it becomes difficult for the converter parallel system to quickly stabilize at the new desired operating point when the system under large disturbance, thus affecting the stability of the energy storage system. To address this issue, the improved passivity-based controller is designed based on the Port-Controlled Hamiltonian with Dissipation (PCHD) model by means of the damping and interconnection injecting. At the same time, the Virtual DC Machine (VDCM) control is adopted to solve the adaptability of improved passivity-based controller, this strategy provides additional inertia and damping to the parallel system of multiple-energy storage converters, while enhancing the dynamic and steady-state characteristics of the system under large disturbances. Finally, simulation and experimental results demonstrate that the proposed control strategy can not only stabilizes the multi-energy storage parallel converter system under large disturbances but also effectively suppresses fluctuations and steady-state errors in the output voltage. Compared to the traditional Interconnection and Damping assignment Passivity-Based Control (IDA-PBC) strategy, it exhibits smaller voltage overshoot, faster adjustment speed, and better dynamic characteristics.