Suitable soil structure and nutrient security are important for plant growth and development. The fractal dimension of soil, along with the distribution of physical and chemical properties and their interactions, plays an important role in studying the stability of soil structures and water and fertilizer cycles. As a sustainable management model, intercropping has positive benefits for erosion control, the spatial optimization of resources, and improving system productivity. The effects of four intercropping methods on the fractal dimension and physicochemical properties of soil were investigated by intercropping Salvia miltiorrhiza with forage and S. miltiorrhiza with forest under typical karst rock desertification habitats in Guizhou. The results showed that the soil nutrient content when intercropping was significantly higher than that of monoculture. The organic carbon content of soil grown under forest is higher than other treatments, and there was a non-significant change in soil water content when intercropping compared with monoculture. The soil fine-grained matter when intercropping was significantly higher than that of monoculture, while the soil fractal dimension showed a tendency to become larger with an increase in fine-grained matter. Intercropping planting, due to its component types and spatial and temporal configurations, leads to differences in soil water and fertilizer interactions, which can be combined with other ecological restoration measures to optimize the composite model and jointly promote the restoration and development of ecologically fragile areas.