An intelligent cooperative control system and method thereof. A parallel structure for low-voltage multi-module permanent magnet synchronous motor cooperative control units is adopted to realize control of low-voltage high power, control of low-speed large torque and system redundancy control; a double-parallel PWM rectifier circuit structure is used, when the system is in unbalanced power supply network environments; a resonant pole-type three-phase soft-switching inverter circuit is used as an inverter unit to improve utilization of DC bus voltage and to greatly reduce device switch losses at high frequencies; a current control and speed estimation unit is used, so that rotor speed and phase angle information is accurately estimated with low cost and high reliability; a controlled object is the multi-module permanent magnet synchronous motor, so that the problems of difficulties in motor installation, transportation and maintenance of a high-power electric drive system and the like are solved.