Over the past century, marine heatwaves (MHWs) have become longer and more frequent under the influence of anthropogenic climate change, with devastating impacts on marine ecosystems. Surface MHWs (SMHWs) and their drivers have been extensively studied using satellite sea surface temperature data, yet the characteristics and mechanisms of subsurface MHWs, especially bottom MHWs (BMHWs) along continental shelves, remain unclear. We compare SMHWs and BMHWs along the continental shelf of China, based on a high-resolution ocean reanalysis dataset, and find that BMHWs are typically longer (0–16 d) and more intense (0°C–50°C days) than SMHWs. The categorisation of both the BMHW and SMHW demonstrates that moderate and strong events are prevalent in most areas with relatively extensive spatial coverage, whereas severe and extreme events occur with relatively limited spatial coverage. There is a clear negative relationship between the BMHW mean intensity and ocean depth along the continental shelf, while the BMHW mean annual days and ocean depth are positively correlated in the Bohai and East China Seas. Generally, BMHWs and SMHWs occur more frequently in shallow coastal regions where the mixed layer depth is more likely to extend to the seafloor, resulting in high BMHW and SMHW synchrony. In addition to spatial coherence, there is a good temporal correspondence between BMHWs and SMHWs across the continental shelf of China from 1993 to 2020.