A hybrid cooling system of a vehicle includes a first cooling system having an engine, a first radiator, and a first water pump. A second cooling system includes a PE system, a second radiator, and a second water pump. A first cooling passage connects the engine and the PE system. A second cooling passage connects the first radiator and the second radiator. A third cooling passage and a fourth cooling passage connect the first cooling passage and the second cooling passage. Three-way valves is provided in the third cooling passage and the fourth cooling passage, respectively, to enable integrated cooling or individual cooling by opening and closing of the three-way valves.