Shallow geothermal energy (SGE) is a renewable energy source that has the advantage of being low-cost, clean, and locally sourced compared to fossil fuels, and is thus significant for China to achieve its future goals of carbon peaking and carbon neutrality. However, determining how to improve the operational efficiency of SGE systems is a key factor in the sustainable development and utilization of geothermal energy. This study examined the long-term operational efficiency of SGE systems and applied numerical simulation methods of hydro-thermal coupling to a SGE utilization project in Shandong Province, China. The effect of the distribution of pumping and injection wells on the operation efficiency of the SGE system was analyzed, and the parameter of operation efficiency, defined by the ratio of the practical minable shallow geothermal energy to the theoretical shallow geothermal energy, was applied to quantify the operation efficiency of the SGE system. The simulated results show that the phenomenon of heat transfixion is significant in the current operation scheme, where one of three pumping wells is located downstream of the study area, which indicates that the local groundwater flow field mainly controls the operation efficiency of the SGE system. In the optimized operation scheme, the distribution of pumping and injection wells can be adjusted according to the feature of groundwater flow and temperature fields. The degree of heat transfixion significantly declines and the operation efficiency increases by 71.5%. In addition, further improvements in the operational efficiency of the SGE system can be considered through the running time. The findings of this paper will be useful for the construction and management of SGE systems.