An exemplary power conversion system includes a first power conversion module, a second power conversion module, and a controller. The first power conversion module includes a first source side converter, a first load side converter, and a first DC link coupled between the first source side converter and the second load side converter. The second power conversion module includes a second source side converter, a second load side converter, and a second DC link coupled between the second source side converter and the second load side converter. The controller is configured to generate a number of switching signals according to a circuit structure of the power source module or a circuit structure of the load module. The switching signals are provided to the first power conversion module and the second power conversion module to balance a first DC link voltage and a second DC link voltage.