The design and optimization of the dewatering scheme for deep foundation pits in a highly permeable heterogeneous layer are critical to protect water resources, control subsidence and mitigate environmental impacts. Numerical simulation is an important and sometimes the only tool in the design of dewatering schemes, especially when the dewatering projects are planned under complex hydrogeological conditions with limited data. The open excavation method was chosen for a project to drain a deep foundation pit (35–44 m) in an upland river valley landscape. Quaternary alluvial deposits (129.0 m thick) are generally distributed in the riverbed and the overburden consists mainly of alluvial-diluvial sandy gravel cobbles, clayey soils, sandy clay, and silty fine sand, making the study area very heterogeneous. There may be water inrush from foundation pit, uneven subsidence and deformation due to the uneven structure of the sand and slope stability. MODFLOW-USG (Unstructured Grid) and Subsidence and Aquifer-System Compaction (SUB) Package were used to create a coupled 3-D groundwater flow-subsidence numerical model for foundation pit dewatering. MODFLOW-USG provides greater flexibility in the design of the grid to achieve a high degree of accuracy in numerical simulation, while effectively reduces computational costs. A combination of waterproof curtain and a partial penetrating well was proposed for lowering the groundwater table. The optimized dewatering scheme with a curtain depth of 60 m and a hydraulic conductivity of 0.00518 m/d, and four rows of dewatering wells with an equal row spacing of 40 m, well depth of 50 m, and well spacing of 12.5 m in each row can meet the dewatering requirements with minimum groundwater discharge in the scenarios. The numerical simulation of this study provides a powerful and useful tool for dewatering and subsidence control of deep foundation pit under complex hydrogeological conditions.