This study proposes a practical control strategy of passivity based control (PBC) of the power conversion system (PCS) used in the energy storage system. First, the differential equations based on the Kirchhoff voltage and current laws are listed in the study, and the mathematical model in Euler-Lagrange form is also given. On the basis of the PBC theory, the system passivity of the PCS is demonstrated, the implementation of differential equations based on the damping injection principle is deduced, and simulation results in SIMULINK are also given. The PBC strategy has the advantages of high stability globally in a nonlinear system, and strong robustness to the system parameters deviation and external interference. Finally, a PCS prototype of 10 kW, which is made up of ac-dc converter and dc-dc converter, is built and the experimental results verify the correctness and effectivity of the proposed solution.