Overground rock is a prominent feature of rocky desertification landscape in karst farmland; however, people often pay attention to their adverse effects, leaving their positive effects on ecohydrological processes and plant growth as rarely studied and utilized. In this study, the effects of overground rock film mulching (ORFM) on soil water flow behavior, soil water content and temporal and spatial heterogeneity were investigated through a dye tracer test and soil moisture measurement. Moreover, the effects of this technology on the root characteristics of crops (maize and broad bean) were analyzed. The results showed that ORFM treatment significantly increased soil water content and its spatio-temporal heterogeneity by preventing preferential flow at the rock–soil interface. It suggested that this practice can provide a more favorable soil moisture environment for crop growth, which was confirmed by the differences in root characteristics of crops (maize and broad bean) under different treatments in this study. It was found that ORFM treatment reduced the root radial extent of crops but increased the root biomass and root bifurcation rate, which are widely considered to be key factors in improving the efficiency of fine root absorption. Therefore, we believe that ORFM has great potential to improve the effective use of soil water and agricultural water management in karst areas, which is essential for sustainable agricultural development in the region.