Electric vehicles (EVs) and the New Energy Microgrid (NEMG) belong to different stakeholders. There can be economic operational problems after EVs are connected to an NEMG. A mathematical model of NEMG multi-objective hierarchical scheduling considering EV orderly charge and discharge behavior and owner’ comprehensive satisfaction is established, and calculation method for analysis is proposed. The EV layer aims to maximize the comprehensive satisfaction of the vehicle owner. The EV charge and discharge plan is established by CPLEX software and transmitted to the NEMG layer. The NEMG layer adjusts the output of controllable distributed generation in the microgrid based on the EV charge and discharge plan to minimize the comprehensive cost of system and interactive power fluctuation. To analyze the high-dimensional, nonlinear and multi-objective model, a multi-objective particle swarm optimization algorithm of a three-black-hole-system capture based on reliability is presented. The simulation results show that the layered architecture of the microgrid with EV can achieve mutual benefit and win-win of EV and NEMG compared with a non-layered architecture. This verifies the validity and effectiveness of the proposed method. This work is supported by the National Natural Science Foundation of China (No. 51607105).