Suitable soil structure and nutrient security are important for plant growth and development, characteristics of soil fractal dimension and distribution of physical and chemical properties and their interactions play an important role in studying the stability of soil structure and water and fertilizer cycles. As a sustainable management model, intercropping has positive benefits for erosion control, spatial optimization of resources, as well as improving system productivity. The effects of four intercropping methods on soil fractal dimension and physicochemical properties 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 soil nutrient content of 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 of intercropping compared with monoculture. The soil fine-grained matter of intercropping was significantly higher than that of monoculture, while the soil fractal dimension showed a tendency to become larger with the increase of fine-grained matter. The 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.