The ground-coupled heat pump is a shallow geothermal exploitation method taking soil as the thermal energy source. The ground heat exchanger is an important component of this system, which includes vertical or horizontal configurations. However, to the best of our knowledge, few studies exist involving the comparison of thermal performances and installation costs of two heat exchanger types considering the influence of ground climate, which makes the selection of heat exchanger configuration challenging for a specific field application. Hence, a 3-dimensional numerical model considering the variations of atmospheric conditions and soil water content is constructed in this paper. Based on this model, the thermal performances and economical efficiencies of vertical and horizontal ground heat exchangers are compared. The results indicate that the thermal performance difference between the two heat exchangers is greater in winter than in summer. The thermal performance is hardly influenced by the injection mass flow rate, while it is considerably affected by the length of heat exchanger. The thermal power rises linearly with the increase in heat exchanger length, and the increment of the vertical ground heat exchanger is higher. In addition, when the heat exchanger length is shorter than 40 m, the installation cost and thereby the total cost of the horizontal ground heat exchanger is considerably higher. With regard to both the thermal performance and economic efficiency, a vertical ground heat exchanger is only recommended when installing a single shallow ground heat exchanger.