Interactions between surface water (SW) and groundwater (GW) have been a focus of watershed hydrology research for a long time. A holistic perspective on integrated SW–GW modeling approach is necessary to understand the hydrological and biogeochemical processes of these two interconnected systems within the watershed. This paper reviewed the progress and coupling strategy of one important SW model (Soil and Water Assessment Tool, SWAT) and GW model (Modular Finite Difference Groundwater Flow, MODFLOW) since 1999. Three main stages of development of coupled SWAT–MODFLOW model are reflected by the high citation of publications by three pioneer studies, which are Sophocleous et al. (1999), Kim et al. (2008) and Bailey et al. (2016). Currently, the research scope of coupled SWAT–MODFLOW models is focused on hydrologic processes, solute transport and the effects of climate change and human activity on water resources. Major uncertainties of SWAT–MODFLOW from model structure, database and parameterization are discussed. In an era of big data, the coupled SWAT–MODFLOW model has great potential to improve understanding of hydro-biogeochemical processes and support sustainable water and ecological management in the watershed.