The access of large-scale electric vehicles (EVs) will increase the network loss of medium voltage distribution network, which can be alleviated by adjusting the network structure and orderly charging for EVs. However, it is difficult to accurately evaluate the charging efficiency in the orderly charging of electric vehicle (EV), which will cause the scheduling model to be insufficiently accurate. Therefore, this paper proposes an EV double-layer scheduling model based on the isolated bidirectional DC−DC (IBDC) converter optimal efficiency model, and establishes the hierarchical and partitioned optimization model with feeder−branch−load layer. Firstly, based on the actual topology of medium voltage distribution network, a dynamic reconfiguration model between switching stations is established with the goal of load balancing. Secondly, with the goal of minimizing the branch layer network loss, a dynamic reconstruction model under the switch station is established, and the chaotic niche particle swarm optimization is proposed to improve the global search capability and iteration speed. Finally, the power transmission loss model of IBDC converter is established, and the optimal phase shift parameter is determined to formulate the double-layer collaborative optimization operation strategy of electric vehicles. The example verifies that the above model can improve the system load balancing degree and reduce the operation loss of medium voltage distribution network.