The pressure fluctuation in nozzle of the common rail injector directly affects the stability of fuel injection. As the pressure fluctuation often the result of coaction of multiple factors, it is difficult to carry out in-depth research. To reveal the mechanism of pressure fluctuation of common rail injector nozzle, based on the verified AMESim simulation model of the injector, the decoupling method of pressure wave in delivery chamber of the injector was investigated by applying the water hammer theory. The water hammer pressure in delivery chamber was divided into four stages, and pressure waves caused by the needle valve opening can be decoupled from that caused by the needle valve closing. In the range of 80–180 MPa rail pressure, both the opening and closing processes of the needle valve are direct water hammer phenomena. It is found that the water hammer pressure of the delivery chamber caused by fuel injection mainly consists of three pressure waves through a series of analysis and simplification. The results show that, all the pressures obtained by the superposition of three pressure waves under different working conditions are in good agreement with the simulated water hammer pressures.