The invention provides a vehicle control system of a plug-in gas-electric hybrid power bus and a control method of the vehicle control system. The vehicle control system comprises a vehicle controller, an engine, a controller of the engine, a clutch, a driving motor, a controller of the driving motor, an auxiliary motor, a controller of the auxiliary motor, a gearbox, a controller of the gearbox, a high-voltage battery, a management system of the high-voltage battery, a high-voltage block terminal, a high-pressure steering system, a high-pressure gas pump system, a high-pressure air conditioner, a direct current / direct current converter, an instrument controller, a starter, a motor water pump, a high voltage control relay and a charging port. The engine is a gas engine. The auxiliary motor is arranged in front of the engine and connected with the engine through a belt. The driving motor is arranged between the engine and the gearbox. A gearbox system is additionally installed behind the driving motor, and a main speed reducer and a vehicle wheel are connected behind the gearbox system. According to the vehicle control system with the vehicle controller as the core, information of a full vehicle and all assemblies is synthesized, on the basis of vehicle and power assembly system modes, the control method is switched and coordinated, the advantages of all subsystems of the plug-in gas-electric hybrid power bus can be fully achieved, and optimal vehicle performance is achieved.