The invention discloses a double multi-level synchronous control method applied to a pulse power inverter. At least two multi-level single-phase full-bridge circuits are synchronously controlled by acontroller. The control method specifically comprises the steps that the controller calculates the switching vector and the duty cycle of two multi-level single-phase full-bridge circuits; the controller carries out combination coding on the switching vector and the duty cycle of two multi-level single-phase full-bridge circuits, and uniformly sends combination codes to an FPGA; and the FPGA decodes the combination codes, and sends a command signal to the driving circuit of each switch device according to the switching vector and the duty cycle of each multi-level single-phase full-bridge circuit. According to the invention, the control complexity of two multi-level synchronously controlled full-bridge circuits is reduced, and the control accuracy and robustness are improved.