The invention discloses a large-scale electric vehicle trunking system based on MMC and a control method thereof. The large-scale electric vehicle trunking system is characterized in that three phase elements composed of an electric reactor, an H-bridge module and a sub-module are connected to an alternating current power grid through an LC filter to form a topological structure of the large-scale electric vehicle trunking system based on MMC, virtual electrical charge states are calculated through the initial electrical charge state, user set standing time and expected electrical charge state of each electric vehicle, the sub-module of the electric vehicle corresponding to a driving signal generated by each carrier signal is determined according to the ranking of the virtual electrical charge states, the differentiation control for electric vehicle charging and discharging power connected to the sub-modules according to user requirements is realized, and the control for three-phase power balance and unit power factors on a power grid side is realized. The system is high in integration degree, high in modularization degree, high in efficiency, little in harmonic distortion, low in switching loss and high in fault-tolerant capacity, and independent control for the sub-modules in each-phase bridge arms can be realized.