【Objective】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 focuses on 2-year-old F.malacophylla seedlings and uses a two factor randomized block experiment to set up different karst habitats, including no stone whole soil (S₀), half stone half soil (S_1/2), and more stone less soil (S_3/4), as well as different rainfall intervals of 3 days (I_3d), 6 days (I_6d), and 9 days (I_9d); Analyze the growth and physiological changes characteristics of F.malacophylla seedlings in different karst habitats. 【Result】The results showed that under the same rainfall time interval, the root biomass of F.malacophylla seedlings increased with the increase of karst fissure thickness (P<0.05), while the stem and leaf biomass showed a trend of first increasing and then decreasing; Increasing the thickness of karst fissures leads to the accumulation of biomass in various organs showed that roots>stems>leaves. Under the treatment of 3d rainfall, the leaf area, leaf circumference, leaf length, leaf width, and potassium (K₊^{), calcium (Ca}₂₊^{), sodium (Na}₊^{), and magnesium (Mg}₂₊^{) contents in various organs of} Fraxinus malacophylla seedlings increased with the increase of karst fissure thickness (P<0.05), while the S_3/4 karst habitat of 6d and 9d rainfall significantly inhibited the leaf traits and accumulation of K₊^{, Ca}₂₊^{, Na}₊^{, and Mg}₂₊^{contents in} F.malacophylla seedlings. Although the increase in thickness of karst fissures inhibits the growth of F.malacophylla seeding, it adapts to different karst habitats through various nutrient transport and physiological regulation strategies, such as increasing root biomass, reducing leaf number (BN), transporting more Na₊ to stems, enhancing Ca₂₊^{and Mg₂₊}nutrient content in leaves, and increasing SOD, POD, and SP enzyme activities to enhance antioxidant enzyme protection systems. Additionally, principal component analysis was conducted on various indicators of the F.malacophylla seedlings, with a cumulative variance contribution rate of 79.26%. Membership function analysis revealed that the I_6dS_1/2 treatment group performed the best, followed by the I_6dS_3/4 group. 【Conclusion】In summary, increasing the thickness of karst fissures during the 3-day and 6-day rainfall intervals can effectively promote the growth of F.malacophylla seedlings, indicating that F.malacophylla seedlings can grow normally in moderate rocky desertification. This study can provide a theoretical reference for the growth strategies and cultivation of F.malacophylla seedlings in different rocky desertification areas.