<p>Changes of tropical cyclones (TCs) under warming climates are of great concern due to their destructive impacts. While changes in TC intensity and rainfall rate have been well documented, far less is known about changes in vertical structure, which are crucial for determining the severity of TC-related hazards. Here, we show that the proportion of shallow cyclones, characterized by convective updraft maxima and low-pressure anomalies confined to the lower troposphere, increases significantly under extreme warm climates. Notably, during the Early Eocene Climatic Optimum (EECO), shallow cyclones are more prevalent than deep cyclones, which dominate in the present-day tropical regions. This transition is primarily driven by strengthened ventilation and increased static stability. Although shallower cyclones tend to generate weaker winds, their collective contribution to extreme rainfall is comparable to that of deep cyclones during the EECO. These findings highlight the necessity of reassessing cyclone-related hydrological hazards, particularly regarding flood risks associated with shallower cyclones.</p>