The invention provides a coal seam step-by-step water injection precise control system and a water injection method and relates to the technical field of coal seam water injection. The system comprises a flow sensor, a pressure sensor, an injection liquid viscosity and pH value sensor, a data monitoring substation and a connection circuit, and real-time transmission of data monitoring is achieved. The coal seam step-by-step water injection precise control system further comprises a high-pressure water pump, a water injection pipe, a check valve, a flow control valve and an electronic control switch, and accurate control over water injection pressure and flow is achieved. The system further comprises a real-time mixing water tank for liquid injection, a plurality of injection liquid modified medicine tanks, a pumping pump, an injection liquid agitator, a steady flow control valve and a water inlet/outlet pipeline, and real-time regulation of and control over the physical properties of the injection liquid are achieved. By the adoption of the structure, based on the mechanical parameter model required for different water injection stages, a controller controls the flow of each component, and the flows are input into the PCL controller in the programming language, so that the real-time monitoring of and control over the step-by-step water injection pressure and flow are achieved, the modified injection liquid required in each stage is optimized, and the coal seam water injection disaster prevention effect is improved.