The invention relates to a water injection well multi-layer separate injection system. The water injection well multi-layer separate injection system includes a ground control system and an underground intelligent water distributor, wherein the ground control system includes a water main pipe, a water branch pipe and a water injection pipe, and a water manual switch valve is installed on the waterbranch pipe through a flange; an upstream pressure transmitter is installed on the upstream of the water manual switch valve, and an intelligent water regulating valve is installed on the downstreamof the water manual switch valve through a flange; the intelligent water regulating valve is provided with a flow sensor, and a water injection manual switch valve is connected to the downstream of the intelligent water regulating valve; the water injection pipe is connected to an outlet of the water injection manual switch valve, and a downstream pressure transmitter is installed on the pipelinebetween an outlet of the intelligent water regulating valve and an inlet of the water injection manual switch valve; signal wires of the upstream pressure transmitter, the downstream pressure transmitter and the intelligent water regulating valve are all connected with a ground controller, and a bypass drainage pipe is connected to the water injection pipe; and an electric pressure relief valve isarranged at an inlet of the bypass drainage pipe. The control system can realize the two-way pressure wave communication between ground equipment and underground instruments.