Rainwater harvesting (WH) and organic fertilizer (OF) are important strategies to alleviate water shortage and soil degradation in rain-fed orchards on the Loess Plateau. However, the integrated mechanism of WH and OF combined with soil improvement has been rarely studied. Therefore, we implemented a novel WHIOF system integrating rainwater collection, supplementary irrigation, and organic fertilizer in a rainfed apple orchard. Five treatments were tested: conventional management (CK), WH only, WH with irrigation (WHI), WHI + low OF (WHIOF1), and WHI + high OF (WHIOF2). The results indicate that: (1) WHIOF significantly improved soil physical properties by reducing soil bulk density (BD), increasing porosity and enhancing saturated hydraulic conductivity (Ks). Organic fertilization elevated soil organic matter (SOM) content and substantially increased the proportion of macroaggregate. (2) WHIOF amplified soil surface charge density (sigma(0)), specific surface area (SSA), and interparticle attraction by modulating electrostatic and van der Waals forces, thereby reducing aggregate disruption (PAD). (3) Water-stable aggregate stability (WGMD) was tightly linked to SOM (r = 0.96, p < 0.01), surface electrochemical properties (e.g., SSA) governed aggregate cohesion. Overall, these improvements in aggregate stability further enhance soil water retention capacity, mitigates erosion risks, optimizes water and nutrient use efficiency, and provides a healthy root environment for apple trees. These findings provide a mechanistic basis for sustainable soil management in rainfed apple orchards, demonstrating WHIOF as an innovative approach to enhance soil fertility and industry sustainability.