Hydrological structural connectivity exerts a critical influence on the transport, distribution, and deposition of runoff and sediment within watersheds. However, its impacts on runoff-sediment relationships remain insufficiently understood. In this study, two typical watersheds Laoshanchong (LSC) and Longyan (LY) in southern China with different hydrological structural connectivity were employed. The hydrological structural connectivity index IC was calculated to quantify hydrological structural connectivity of the watersheds. Four hysteresis types such as clockwise, anticlockwise, figure-eight, and complex, were conducted based on 185 flood events for exploring the runoff-sediment hysteresis relationships under different hydrological structural connectivity. The results showed that the hydrological structural connectivity of LSC was higher, with higher IC values ranging from -7.49 to 8.72 (ICmean of 2.38). Its predominant hysteresis type was clockwise (46.34%). Clockwise and complex hysteresis events were the main contributors to runoff and sediment yield in LSC, resulting in the strongest runoff and sediment yield capabilities, respectively. In LY, the IC ranged from -11.65 to 4.08 (ICmean of -1.88), indicating low hydrological structural connectivity. The distribution of runoff-sediment hysteresis type was relatively uniform, with no single type dominates. Complex events were the major contributors to runoff and sediment yield in LY. It can be concluded that different hydrological structures determine the variability in runoff-sediment dynamics within watersheds. Therefore, differentiated and targeted treatments should be implemented in the integrated management of water and soil erosion. These findings provide theoretical basis and practical guidance for the restoration and management of the basin ecological environment.