Anemone shikokiana is a rare species adapted to two heterogeneous habitats including conifer and broad-leaf mixed forest and shrubs of mountaintop at higher than 600 m elevation. In the present study, we chose five sample transects to explore the response mechanism of this species to heterogeneous habitats and altitude gradients. Leaves, which are plant organs with the largest surface area exposed to the sun and air, are the main photosynthetic organs and sensitive organs to environmental changes. The morphology and anatomical structure of the leaves in A. shikokiana were analyzed by the paraffin section method and microscopic technique. We observed the morphological characteristics of the leaves and epidermal hairs, measured the thickness of the leaves and mesophyll tissue, calculated their anatomical indices and stomatal parameters, and analyzed the correlation between these characteristics and the heterogeneous habitats or altitude. Compared with those of leaves from mountaintop shrubs, the density of upper and lower epidermal hairs, specific leaf area, and relative opening of the stoma of leaves from the conifer and broad-leaf mixed forest were greater, whereas stoma density, leaf thickness and palisade and spongy tissue thickness were lower. The length of upper epidermal hairs and relative opening of the stoma gradually decreased with increasing altitude. However, there was no obvious regularity between the other parameters measured and different altitude, such as palisade and spongy tissue thickness, specific leaf area, and stomatal index. This study provides a theoretical foundation for the protection and utilization of A. shikokiana and provide references for related research in other plants.