Abstract: The heat exchange of a single-well cycling ground heat exchange system is mainly affected by thermal conduction, by forced convection, and by thermal dispersion. In addition, the skin effect around the well has a significant impact on extraction and injection of the groundwater. Therefore, analyzing the groundwater flow is crucial to study the heat exchange in geothermal systems. In view of this, a seepage model is established upon the heterogeneous skin effect. The solutions of the groundwater drawdown in the Laplace domain are derived by using the finite Fourier cosine transform and Laplace transform, and the solutions in the time domain are obtained by using the Laplace numerical inversion methods. The correctness of the solutions is verified through degradation analysis and numerical simulation. Different radial hydraulic conductivity variation patterns are proposed to characterize the heterogeneous skin effect, and the influences of relevant parameters on the groundwater drawdown are explored. The research results show that: the skin effect has a significant impact on the groundwater drawdown in the skin zone, while its influence on the groundwater drawdown in the formation zone can be neglected. Compared with the homogeneous skin zone, the groundwater drawdown caused by the positive heterogeneous skin is smaller, while the groundwater drawdown caused by the negative heterogeneous skin is larger. Moreover, the length of the pumping and injection zones and the flow rate of the injection zone also have significant impacts on the groundwater drawdown. The newly derived seepage model for single-well cycling ground heat exchange system can effectively describe the radial heterogeneity of the skin zone and provide an analysis method for engineering applications.