The invention discloses an engine crankcase ventilation system provided with a bypass protection structure. The engine crankcase ventilation system provided with the bypass protection structure comprises an air cylinder head cover assembly and a crankcase ventilation system connected with the air cylinder head cover assembly. The crankcase ventilation system is connected with an air intake manifold resonant cavity through a pipeline. A bypass valve is arranged between an air outlet of the air cylinder head cover assembly and an air intake manifold assembly and is connected with the crankcase ventilation system in parallel. When the pressure of the air cylinder head cover assembly is higher than external atmospheric pressure in position, the bypass valve turns on. The bypass valve is higher than the air outlet of the air cylinder head cover assembly. When the crankcase ventilation system is shut down, the pressure of a crankcase rises, the bypass valve turns on, the air in the crankcase enters the air intake manifold assembly, the pressure of the crankcase drops to negative pressure, and then the bypass valve turns off. The bypass protection structure can turn on or turn off according to the relation between the pressure of the crankcase and the atmospheric pressure so that the pressure of the crankcase can be adjusted to become negative pressure, and consequently reliable operation of a whole engine can be guaranteed.