Subsurface runoff in a land surface model is usually parameterized as a single-valued function of total storage in a basin aquifer reservoir. This kind of parameterization is often sin-gle-valued function of storage-discharge under a steady or “quasi-steady” state, which cannot rep-resent the influence of aquifer recharge on subsurface runoff generation. In this paper, a new sub-surface runoff parameterization with water storage and recharge based on the Boussinesq-storage equation is developed. This model is validated by a subsurface flow separation algorithm for an ex-ample river basin, which shows that the new model can simulate the subsurface flow reasonably. This kind of parameterization is often sin-gle-valued function of storage-discharge under a steady or “quasi-steady” state, which can not rep-resent the influence of aquifer recharge on subsurface runoff generation. In this paper, a new sub-surface runoff parameterization with water storage and recharge based on the Boussinesq-storage equation is developed. This model is validated by a subsurface flow separation algorithm for an ex-ample river basin, which shows that the new model can simulate the subsurface flow reasonably.