The ground-water heat-pump system (GWHP) provides a high efficient way for heating and cooling while consuming a little electrical energy. Due to the lack of scientific guidance for operating control strategy, the coefficient of performance (COP) of the system and units are still very low. In this paper, the running strategy of GWHP was studied. First, the groundwater thermal transfer calculation under slow heat transfixion and transient heat transfixion was established by calculating the heat transfer simulation software Flow Heat and using correction factor. Next, heating parameters were calculated based on the building heat load and the terminal equipment characteristic equation. Then, the energy consumption calculation model for units and pumps were established, based on which the optimization method and constraints were established. Finally, a field test on a GWHP system in Beijing was conducted and the model was applied. The new system operation optimization idea for taking every part of the GWHP into account that put forward in this paper has an important guiding significance to the actual operation of underground water source heat pump.