The invention relates to the technical field of electromobile charging, particularly to an electromobile charging system based on new energy application and a control method thereof. An electromobile charging station micro-grid system is composed of a new energy power supply system, a reserve diesel power supply system and an energy storage system. The new energy power supply system includes one or more of a photovoltaic power supply system, a wind power supply system and the like. The electromobile charging station micro-grid system is controlled by an intelligent control system, in case of normal mains supply, the new energy power supply system is subjected to networking operation with mains supply to power electromobile charging piles in the manner that the new energy power supply system is a priority; in case of mains supply outage or failure, connection with the mains supply is cut, and the electromobile charging piles are power by the new energy power supply system, the diesel power supply system and the energy storage system. In this way, power pressure, caused by additional power load capacity of the electromobile charging station, is balanced, an intelligent electromobile charging system safe, reliable and free of noise and pollution is established, and the electromobiles are charged in the energy-saving and emission-reducing manner.