The invention provides a virtual synchronous machine control system and method based on a power electronic transformer. The system includes a high-voltage-side MMC, an isolated DC/DC converter and a battery pack. The MMC converts the three-phase AC voltage at a high-voltage side into high-voltage DC voltage. The main function of the isolated DC/DC converter is to convert the high-voltage DC voltage obtained by the MMC into low-voltage DC voltage. The virtual synchronous machine control system can meet the requirements of a large-capacity virtual synchronous machines (above 5MW) with low switching frequency and low loss, requires no isolation transformer, achieves high efficiency, realizes low harmonics by using a MMC multilevel structure at a DC/AC side, achieves DC output less than DC1000V to meet a lithium battery voltage range requirement, and is low in cost, easy to implement. Moreover, the virtual synchronous machine control system can realize the functions of primary frequency modulation, inertial damping and reactive voltage regulation, and the control method is flexible.