The invention relates to a cooling system of a motorboat engine, comprising a water pump assembly, a cooling water channel water chamber of the engine body cylinder body cover, an intake pipe joint and a thermostat seat, a general oil pan, an exhaust pipe and an auspuff flange and a sound attenuating system. The heat of the engine is transformed into the internal energy of cooling water and then discharged out of the motorboat; the cooling water pumped by the water pump assembly is divided into two ways which respectively cool the engine body, the general oil pan and an exhaust system comprising the exhaust pipe and the auspuff flange; the basic flow of the cooling water in the cylinder body cover is that the water flows from the bottom end part of the engine body to the top end part of the engine. By the adoption of the invention, the heat generated in the running process of the engine is transmitted to the cooling water instead of being emitted directly, and finally is discharged out of the motorboat by the cooling water, therefore, the cooling is reliable, the service performance and the safety performance of the motorboat are not affected by the gathering of a great deal of heat in the motorboat, thus conforming with the requirement of the motorboat engine to the cooling system.