The invention discloses a control system and a method of a diesel engine main power supply in an independent microgrid. A diesel generator main power supply in-place self-government main control module is used for monitoring active power and reactive power of a diesel engine outlet, and is combined with a steady-state operation point to judge whether active power constraints, reactive power constraints, active power excess, reactive power excess and power fluctuation situation exist; if yes, a constraint and fluctuation behavior is judged, and a power P/Q instruction of an energy storage system is adjusted, so that the power of the diesel generator main power supply outlet is recovered and stabilized to be near the steady-state operation point; if not, the diesel generator main power supply in-place self-government main control module is used for continuously monitoring and judging. According to the control system and the method of the diesel engine main power supply in the independent microgrid provided by the invention, the disturbance of renewable energy source intermittent fluctuating power on the diesel engine main power supply is reduced, the problems of inverse reactive power, inverse active power and outlet power rapid fluctuation occurred on a diesel generating set are solved, and long-time and stable operation of the independent microgrid with high renewable energy source permeability and high-quality electric energy supply are realized.