Red mud, a solid waste of alumina extraction from bauxite, was used as a compost carrier to prepare a geological fertilizer. It was amended at proportions of 0, 5%, 10%, 15% and 50% by weight (g/kg) to improve a rocky desertification soil (classified as lime soil) productivity. Through the simulation of different rain intensity (15, 50, and 90 mm/h) with three precipitation rates (1000, 2000, 3000 mm), soil chemical and physical properties, such as soil organic matter (SOM), total nitrogen (TN), ammonia nitrogen (AN), nitrate nitrogen (NN), total potassium (TK), available potassium (AK), total phosphorus (TP), available phosphorus (AP), bulk density and aggregates were tested and analyzed. In addition, a three-dimensional evaluation and analysis of the improvement attributed to the geological fertilizer was conducted. The results showed that the soil loss could be maintained in the range of 19%–72% under rainfall intensities. In addition, the reduction rate of soil clay content was less than 20%, and the lowest reduction rate of SOM, TN, TP and other nutrient was only 4% at the application rate of 5%–50%. The BD of the 0–20 cm top soil decreased progressively from 1.2 to 0.9 g/cm³, while the water-stable aggregate volume increased by 45%–76%. The red mud-based fertilizer enhanced the ability of the rocky desertification soil to resist rainfall erosion and infiltration in amended soil profiles. Considering the trends of nutrient losses and effects on the soil structure, the application rate of 15% by weight (g/kg) was best for improving the rocky desertification soil productivity.