Drought is increasingly common due to frequent occurrences of extreme weather events, which further increases soil water repellency (SWR). It could reinforce the effect of SWR on soil functions under conservation tillage systems. However, the relationship between SWR and soil hydrological function is still unclear. We studied the impacts of SWR and soil structure on soil hydrological function. Three treatments were conducted in a long-term tillage experiment: conventional tillage (CT), reduced tillage (RT), and no-tillage (NT). Tillage, soil depth, and growth period had significant influences on SWR, soil structure (i.e., penetration resistance [PR], total porosity [TP], and mean weight diameter [MWD]), and soil hydrological functions (i.e., water storage, least limiting water range [LLWR], and plant available water). Compared to CT, NT and RT increased the water repellency index (RI) in 0-20 cm by 13.8%-40.1% and 6.5%-18.2% during the growth period. RI played a prominent role in increasing soil water storage compared to soil TP, PR, MWD, and SOC. PR was the most critical influence on LLWR compared to other variables. A structural equation model revealed that SWR directly affected soil hydrological function, whereas the effect of SWR (0.24) was smaller than that of soil structure (0.67). In addition, soil structure had a direct influence on SWR, indicating that the effect of SWR could be regulated by soil structure. Overall, this study showed a link between SWR and soil hydrological function and provides deeper fundamental insights into the role of SWR on the sustainability of conservation tillage.