The invention discloses an intelligent engine cooling system based on reverse cooling and a control method. The cooling system comprises a complete machine water jacket, an electric control water pump, an electronic thermostat, an electric control fan, a heat radiator, an expansion water tank, a temperature sensor, a motor and an electronic control unit. In the system working process, a cooling liquid is pumped into an engine by the electric control water pump, enters from the top of a cylinder cover water jacket, flows from top to bottom, flows into the complete machine water jacket after cooling a cylinder cover and flows out after cooling a cylinder jacket; and the electronic thermostat is used for distributing the flow rate of the cooling liquid entering large and small circulation according to the temperature of the cooling liquid of a main pipe, and the cooling liquid is pumped into the engine and is cooled after being circulated. By using the intelligent engine cooling system based on reverse cooling, the temperature of the cooling liquid for the cylinder cover can be reduced, the temperature of the cooling liquid for the cylinder cover is increased, meanwhile, the heat exchange coefficient of the cylinder cover water jacket is increased, so that the thermal states of the cylinder cover and the cylinder jacket are improved.