Caragana microphylla, Caragana intermedia, and Caragana korshinskii are perennial shrubs and geographically alternative species distributed from East to West on the Inner Mongolia Plateau. The species are of great significance in ecology and have a high forage value. In this study, 13 populations of the three Caragana species were observed with a scanning electron microscopy (SEM), and the effects of climatic factors and soil factors on the differentiation of the leaf epidermis were analyzed. The results showed that three species of Caragana were densely covered with epidermis and stomata with stratum corneum, which are characteristics of drought resistance. From East to West, the three Caragana species demonstrated an increase in density of epidermis hair and a decrease in stomatal density of the upper epidermis. There are apparent differences in leaf epidermis micromorphology among populations which vary with the environmental changes. The stepwise regression analysis showed that annual precipitation, effective accumulated temperature, sunshine hours, total soil nitrogen, total phosphorus, and soil organic carbon have a significant influence on the changes of epidermal micromorphology. The above results showed that the climatic and environmental factors significantly affect the micromorphological characteristics of the epidermis of the three species of Caragana and that the adaptative differentiation takes place in the epidermal micromorphology. This study provides a theoretical basis for predicting the adaptation mechanism, protection, and utilization of plants in the context of global climate change.