Rubber is usually grown as a monoculture but there have been recent attempts to encourage rubber-based agroforestry systems to reduce adverse environmental impacts, including the reduction of soil erosion in Xishuangbanna, SW China. To estimate the influence of different types of rubber-based agroforestry systems on soil erosion processes, we measured the throughfall kinetic energy (TKE) under different vegetation types by using 640 sand-filled Tübingen splash cups. This study was conducted in Xishuangbanna Tropical Botanical Gardens under natural rainfall conditions. Our results indicated that in both rubber-based agroforestry systems and rubber monocultures, a significant linear positive correlation exists between TKE and rainfall amount. Rainfall amount is a critical factor that contributes to soil detachment in rubber plantations in this region. TKE under rubber plantation conditions was found to be notably higher than under open field conditions (ranging from 1.84 to 2.32 times greater). However, there was no significant difference under multiple canopies compared to monoculture. TKE values under the different rubber-based agroforestry systems were closely related to the canopy structure, and TKE and leaf area index were significantly negatively correlated. The spatial variability of TKE was higher in rubber-based agroforestry systems than in rubber monocultures. In addition, TKE was usually concentrated in 3–4 m bands that did not have the protection of a sub-canopy. The fact that the erosion by TKE under rubber-based agroforestry was still high highlights the importance of selecting intercrops when constructing rubber-based agroforestry systems and of improving planting patterns.