As a major and popular groundwater extraction structure, seepage wells are often used to transfer river water into aquifers for harvesting water resources. It can help ameliorate the imbalance between supply and demand, especially in areas of water shortage. Large drawdowns due to pumping may cause the river to disconnect from the groundwater and to form an unsaturated zone, which seriously affects the efficiency of seepage wells. However, most of the current models of extraction structures of non-tube wells only account for saturated flow and do not consider unsaturated conditions. To address this limitation, a saturated-unsaturated coupling model has been developed using the exchange flow rate between the well pipe and the aquifer as the coupling point. Moreover, the model was evaluated with physical simulation test data. The statistical results indicated that the model can estimate the drawdown and pumping rate well with root-mean-square deviations (RMSD) of 0.0114 m and 0.0079 L/s, respectively, for a river with strong leakage capacity, and 0.0129 m and 0.0099 L/s, respectively, for a river with weak leakage capacity. The critical drawdown, where the river disconnects from the aquifer, as well as variations of the unsaturated zone, is also discussed. The present study provides important information for the design of seepage wells with reasonable drawdown while being able to predict the potential water yield, and at the same time help protect the groundwater environment.