The invention discloses an intelligent cooling system based on split cooling and reverse cooling for an engine, and a control method. The cooling system comprises a cylinder cover water jacket, a body water jacket, an electronically-controlled water pump, electronic thermostats, an electronically-controlled fan, a heat dissipater, an expansion water tank, temperature sensors, motors and an electronic control unit. During a working process of the system, the electronically-controlled water pump pumps a cooling liquid in the engine, the first electronic thermostat controls the cooling liquid to enter the cylinder cover water jacket and the body water jacket according to cooling liquid temperature signals of a cylinder cover and a body respectively, flow from top down, and flow out after the cooling the cylinder cover and the body; and the second electronic thermostat distributes the flow rate of the cooling liquid entering large circulation and small circulation according to a cooling liquid temperature of a main tube, and the cooling liquid is circulated and then pumped in the engine to cool. The cooling system disclosed by the invention is capable of accurately distributing the flow rate of the cooling liquid in the cylinder body and the body of the engine, reducing the phenomenon of non-uniform cooling, and shortening the warm-up time of the engine; and the heat states of heated components are optimized through the reverse cooling.