In order to analyze the rationality of the compound well structure and the degree of heat penetration of groundwater in a groundwater ground source heat pump project in a certain district of a city, the author proposed a method for building energy consumption simulation and groundwater flow numerical model. The variation trend of groundwater temperature under different heat transfer temperature difference is simulated and predicted. The experimental results show that the fitting points where the error between the simulated predicted temperature and the actual measured temperature does not exceed 0.5?C account for 51.7%, the fitting points where the error is 0.5~1?C account for 28.7%, the fitting points where the error is 1~2?C account for 18.1%, and the fitting points where the error is greater than 2?C account for 1.5%. The dynamic change trend of the simulated predicted temperature curve is basically consistent with that of the actual measured temperature curve. It is proved that the building energy consumption simulation and the numerical model of groundwater flow can effectively analyze the rationality of the compound well structure of the groundwater ground source heat pump project and the degree of groundwater heat penetration.