Anthropogenic climate change has exacerbated soil moisture droughts globally, yet this exacerbation in their spatiotemporal evolution in terms of soil vertical structure remains unclear. Here we propose a Lagrangian four-dimensional tracking framework to identify a type of spatial (horizontal and vertical)–temporal contiguous drought events, that is, deep droughts characterized by bottom-heavy deep-dominated shapes, with more extensive moisture deficits in deep than surface soils. These deep droughts, accounting for a quarter of total events, are ignored in surface-based soil moisture monitoring. Both reanalyses and climate models show significantly increasing duration and intensity of the deep droughts over the past four decades, attributable to anthropogenic climate change. Relative to the past, future deep droughts are projected to become longer-lasting and more intense globally, with larger increases in deeper soil layers under higher-emission scenarios. These deep droughts hidden below the surface pose challenges for satellite-based agricultural drought monitoring and cause an underestimation of adverse impacts of droughts on ecosystems.