【Objective】This study aimed to explore the response of functional traits of leaves and the antioxidant enzymes of Fraxinus malacophylla seedlings to rainfall characteristics in different rocky desertification habitats.【Method】This study focused on 2-year-old F. malacophylla seedlings and adopted a two-factor randomized block design. Different karst habitats were set up, including no stone whole soil S0 (all soil layers), half stone half soil S1/2 (upper 1/2 was soil layer, lower 1/2 was Karst layer), and more stone less soil S3/4 (upper 1/4 was soil layer, lower 3/4 was Karst layer), as well as different rainfall time intervals of 3 days (I3d), 6 days (I6d), and 9 days (I9d). During the experiment, the growth and physiological changes characteristics of F. malacophylla seedlings in different Karst habitats were analyzed.【Result】The results showed that under the same rainfall time interval, the root biomass of F. malacophylla seedlings increased with the increase of rock coverage (P<0.05), while the stem and leaf biomass showed a trend of first increasing and then decreasing. As the thickness of Karst increases, the biomass accumulation of various organs from high to low was in the order of roots, stems, and leaves. Under a 3-day rainfall treatment, the leaf area, leaf circumference, leaf length, leaf width, and potassium (K+), calcium (Ca2+), sodium (Na+), and magnesium (Mg2+) contents in various organs of F. malacophylla seedlings increased with the increase of rock coverage (P<0.05). Also, the S3/4 Karst habitat with 6-day and 9-day interval rainfall significantly inhibited the leaf traits and accumulation of K+, Ca2+, Na+, and Mg2+contents in F. malacophylla seedlings. F. malacophylla seedlings adapt to different Karst habitats through various physiological and biochemical regulation strategies, including biomass allocation optimization, interorgan nutrient transport strategies such as Na? transfer to stems, Ca2?/Mg2? enrichment in leaves, reduction of leaf number (LN), activation of superoxide dismutase (SOD), and peroxidase (POD) enzyme activities, and increase soluble protein (SP) content.【Conclusion】In summary, a 6-day rainfall interval and a half stone and half soil habitat (I6dS1/2) are the optimal combination for seedling growth. This study provides a theoretical basis for the cultivation and promotion of F. malacophylla seedlings under different levels of rocky desertification in the southwestern Karst region. It is recommended to adopt a water replenishment interval of about 6 days for afforestation and nurturing in areas with moderate rocky desertification.