The invention provides a main controller of a natural gas power station compensation device and a control method of the main controller, and belongs to the technical field of control over the natural gas power station compensation device. The problem that a current inverter controller applied to a large power grid can not adapt to the complex power grid environment is solved. The control method is realized through a main control module of the main controller and collected signals. The control method comprises the steps that collected three-phase alternating-current voltage is monitored synchronously, positive and negative sequence components of a synchronous rotating coordinate system are obtained, and grid connection current giving is achieved according to set active power assignment and reactive power assignment; the system capacity restraint is used for correcting the grid connection current giving; then phase angle lagging of grid connection currents is corrected; then a current instruction is converted to a fundamental wave positive sequence synchronous rotating coordinate system, and guided into a current control loop; finally, positive sequence PARK inverse transformation is carried out on currents output by the control loop, and an SVPWM algorithm is applied to obtain control pulses of a three-phase inverter bridge so that an inverter can be controlled to output the expected currents. The main controller is applied to a natural gas power station.