Climate variability and human activities are major influences on the hydrological cycle. However, the driving characteristics of hydrological cycle changes and the potential impact on runoff in areas where natural forests have been converted to rubber plantations on a long-term scale remain unclear. Based on this, the Mann–Kendall (MK) and Pettitt breakpoint tests and the Double Mass Curve method were employed to identify the variation characteristics and breakpoints of precipitation (P), potential evapotranspiration (ET0), and runoff depth (R) in the Wanquan River Basin (WQRB) during the 1970–2016 period. The changes in runoff attributed to P, ET0, and the catchment characteristics parameter (n) were quantified using the elastic coefficient method based on the Budyko hypothesis. The results revealed that the P and R in the WQRB exhibited statistically insignificant decreasing trends, while ET0 displayed a significant increasing trend (p < 0.05). The breakpoint of runoff changes in the Jiabao and the Jiaji stations occurred in 1991 and 1983, respectively. The runoff changes show a negative correlation with both the n and ET0, while exhibiting a positive correlation with P. Moreover, it is observed that P and ET0 display higher sensitivity towards runoff changes compared to n. The decomposition analysis reveals that in the Dingan River Basin (DARB), human activities account for 53.54% of the runoff changes, while climate variability contributes to 46.46%. In the Main Wanquan River Basin (MWQRB), human activities contribute to 46.11%, whereas climate variability accounts for 53.89%. The research findings suggest that runoff is directly reduced by climate variability (due to decreased P and increased ET0), while human activities indirectly contribute to changes in runoff through n, exacerbating its effects. Rubber forest stands as the prevailing artificial vegetation community within the WQRB. The transformation of natural forests into rubber plantations constitutes the primary catalyst for the alteration of n in the WQRB. The research findings provide important reference for quantifying the driving force of hydrological changes caused by deforestation, which is of great significance for sustainable management of forests and water resources.