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Drought is a critical limiting factor of plant growth, and plants living in arid areas must develop adaptation mechanisms to resist drought stress. In this study, we studied the drought resistance mechanisms of two tree species, Triadica rotundifolia and Cinnamomum burmannii, based on their foliar physiological and anatomical characteristics. These trees are indicator plants in the limestone region of southern China. We evaluated and compared the changes in the contents of chlorophyll, soluble protein, soluble sugars, proline, malondialdehyde (MDA), proline, activity of superoxide dismutase (SOD) and peroxidase (POD), chlorophyll fluorescence parameters, and leaf anatomical structure between these two species. The results showed the following. (1) The content of Chl(a+b), soluble protein, soluble sugar and SOD activity of the two species’ seedlings had an increasing trend at first and then a decrease over the entire drought experiment. The change in MDA content was more sensitive in T. rotundifolia, and the peak (33.05 mmol.ml(-1)) appeared on the 28th day of the drought experiment. Comparatively, the proline content and POD activity were more sensitive in C. burmannii, and the proline peak (217.11 mu g.g(-1)) appeared on the 24th day. (2) Under the continuous drought stress, the electron transport rate of the seedlings decreased, whereas the non-photochemical quenching showed different trends for the different species. Severe drought stress in T. rotundifolia caused an increasing trend in the light energy capture efficiency (F-v/F-m), while it declined continuously in C. burmannii. (3) Under the drought stress, the leaves of T. rotundifolia became thicker. The arrangement of spongy tissues became loose, and the ratio of palisade to spongy tissue decreased. However, the leaves of C. burmannii showed a few different features, such as inconspicuous differentiation between palisade and spongy tissues, a high loose degree of leaves, and low packing. (4) The leaf physiological indices had a strong relationship with the anatomy characteristics, as revealed by principal component analysis (PCA); the adaptability to drought tolerance of T rotundifolia was stronger than C. burmannii. In conclusion, T rotundifolia is better able to adapt to drought conditions due to its physiological and anatomical characteristics, which allow the species to better buffer drought-induced physiological responses and variability in leaf structure.