Drainage is a crucial soil hydrological process that governs the partitioning of rainfall into runoff, groundwater recharge, soil water storage and evapotranspiration. Despite its significance, the drainage process is poorly understood due to the difficulty in direct measurements and insufficient understanding of its underlying physical mechanisms. To address these challenges, we present an innovative, physically-based, data-driven approach, SM2D (Soil Moisture to Drainage), to estimate drainage. SM2D was applied and examined using soil moisture data from a large-scale observation network over mountainous areas during 2014–2020. The soil moisture threshold governing drainage initiation proves to be significantly lower than the commonly employed field capacity metric in hydrological models. This threshold is influenced by factors such as mean soil moisture, bulk density, residual soil moisture, soil organic carbon, and parameters n and α of soil retention curve. Notably, field capacity has minimal impact on this threshold. Additionally, our analysis reveals that the drainage process is more influenced by the Soil Water Storage Increment (SWSI) than by mean soil moisture (MSM) that has traditionally been recognized as a key factor in drainage control. In comparison to commonly used exponential equations and those in models such as the Soil & Water Assessment Tool (SWAT), SM2D demonstrates superior performance in estimating drainage. The exponential equation derived from the SWSI outperforms those derived from other soil moisture metrics, including the commonly utilized MSM, challenging prevailing norms in drainage equations. SM2D holds the potential to generate extensive drainage datasets from satellite or large-scale soil moisture observations, advancing large-scale hydrological studies.