Severe soil-water loss and unfertile soil frequently occur under karst desertification environments. The surface-underground dual structure in these areas allows the surface water to leak into the subsurface through cracks and sinkholes, as well as other conduits, causing a special “karst drought”. Hence, water-resource shortage has become a challenge for local agricultural development. To realize efficient utilization of water resources, an urgent need is to clearly understand and study the law of farmland hydrological cycles under agroforestry practices, which is still understudied. Here, we focused on the hydrological cycle at the farmland scale and water-saving measures under agroforestry in three study areas representing different degrees of karst desertification. First, a significant positive correlation was found between total and available precipitations as well as land evapotranspiration (LET). Second, under agronomic measures, the soil water content in the three areas was all higher than that of the control group while soil evaporation was all lower. This indicates that agronomic measures can contribute to the efficient use of water resources by halting soil evaporation and increasing soil water content. Third, dwarf dense planting and pruning technologies were helpful in inhibiting crop transpiration and reducing vegetation interception. Fourth, in the farmland hydrological cycle of agroforestry, 77.45% of precipitation transformed into soil water storage, 24.81% into soil evaporation, 20.73% into plant transpiration, 17.40% into groundwater, and 5.18% into vegetation interception. However, their sum was greater than 100%, suggesting that the farmland-scale water cycle is an open system. The implication is that different agronomic practices under agroforestry bring certain water-saving benefits by constraining the conversion of ineffective water and promoting the storage of effective water, thus opening up promising opportunities for efficiently utilizing water resources in karst desertification areas. The finding is also significant to the control of karst desertification, soil and water conservation, and karst drought alleviation.