Neutral beam injection heating is one of the main auxiliary heating methods in controllable nuclear fusion research. In the EAST neutral beam injector, a water flow calorimetry(WFC) system is applied to measure the heat load on the electrode system of the ion source and the heat loading components of the beamline. Due to the heat loss in the return water pipe, there are some measuring errors for the current WFC system. In this paper, the errors were measured experimentally and analyzed theoretically, which lay a basis for the exact calculation of beam power deposition distribution and neutralization efficiency. Neutral beam injection is one of the main auxiliary heating methods in controllable nuclear fusion research. In the EAST neutral beam injector, a water flow calorimetry (WFC) system is applied to measure the heat load on the electrode system of the ion source and the Due to the heat loss in the return water pipe, there are some measuring errors for the current WFC system. In this paper, the errors were measured experimentally and analyzed theoretically, which lay a basis for the exact calculation of beam power deposition distribution and neutralization efficiency.