The present invention relates to the technical field of pulsed power. Disclosed is an anti-electromagnetic-interference module control system for a modular pulsed power supply, which system aims to achieve the purposes of ensuring, by means of the anti-electromagnetic-interference module control system, that in a high-voltage large-current complex electromagnetic environment, 129 modules of the modular pulsed power supply can stably and reliably execute an instruction that is sent by the control system, and upload state parameters of all discharging modules and chargers to the control system, so that excitation currents that have various types of output time sequences and are flexibly adjustable can be provided for 18 coils. The system comprises: a remote control system, a data storage system, an optical fiber switch, an uninterruptible power supply, a local controller, a discharging module controller and a charger controller. By means of the present invention, a modular pulsed power supply has a good electromagnetic compatibility in a high-voltage large-current complex electromagnetic environment.