The invention discloses an active power filter control system with modularized parallel processing. The system includes a display, a main control panel, a first slave control panel, a second slave control panel, a third slave control panel, a voltage sensor and a current sensor, the main control panel is connected with the display, the voltage sensor, and the current sensor, and the main control panel is connected with the first slave control panel, the second slave control panel and the third slave control panel. The invention also discloses a control method of the active power filter control system with modularized parallel processing. According to the control method, for industrial occasions, three-phase loads are used, high speed parallel processing capability of an FPGA is utilized to implement three-phase modularized control and perform parallel detection and processing on three-phase harmonic current, thereby shortening a computing period, increasing the number of times of harmonic detection within a certain time, improving detection precision, and satisfying various load requirements.