Increasing total soil porosity and optimizing pore distribution improve soil water-holding capacity, thereby alleviating drought impacts on crop yields in semi-arid regions. A three year split-plot field experiment was conducted, with organic fertilizer (sheep manure) rates as main plots and water-retaining agent (WRA) rates as subplots. Four organic fertilizer (0, 45, 60, and 75 Mg hm(-2)) and four WRA rates (0, 0.3, 0.6, and 0.9 Mg hm(-2)) were set, resulting in 16 combined treatments. Undisturbed soil samples were collected to analyze pore distribution and water availability using the soil water retention curve. The results showed significant variations in ameliorative effects with soil depth. Individual applications of either organic fertilizer or WRA significantly improved topsoil pore distribution and water availability but exerted negative effects on the subsoil. Combined application enhanced both soil layers, with a stronger synergistic effect in the subsoil. The combination of 45 Mg ha(-2) organic fertilizer + 0.9 Mg ha(-2) WRA achieved optimal soil improvement in the 0-20 cm layer, increasing aeration porosity by 21.89% compared to organic fertilizer alone; this improvement led to 14.99% and 15.65% increases in plant available water (PAW) and readily available water (RAW), respectively. For the 20-40 cm layer, the combination of 60 Mg ha(-2) organic fertilizer + 0.9 Mg ha(-2) WRA was optimal, increasing total, aeration, and capillary porosity by 24.18%, 183.50%, and 56.73%, respectively, compared to organic fertilizer alone. Consequently, subsoil water availability was enhanced, resulting in 57.53% and 61.18% higher PAW and RAW than the control without WRA. These findings highlight the necessity of layer-specific regulation and differentiated management. The optimal combinations (OF45+W0.9 for 0-20 cm and OF60+W0.9 for 20-40 cm) effectively optimize pore distribution and increase water availability through the complementary synergistic effects of organic fertilizer and WRA. Consequently, this strategy alleviates drought stress on crop yields in semi-arid regions.