The selection of tree species is critical for restoring ecosystem functions in degraded forests, yet the impacts of native species reintroduction on belowground microbial processes remain poorly understood, particularly across soil profiles. Here, we measured the potential activities of two C-acquiring enzymes (beta-1,4-glucosidase and beta-D-cellobiosidase), two N-acquiring enzymes (beta-N-acetylglucosaminidase and leucine aminopeptidase), and one organic-P-acquiring enzyme (alkaline phosphatase). Using variance analysis, correlation analysis, redundancy analysis (RDA), random forest analysis (RFA), we quantify and compared the variations in microbial resource limitations in 0-10 cm surface and 20-30 cm subsurface soils following converting Eucalyptus to six native tree species plantations. Results showed that after conversion to native tree species, surface C-acquiring enzyme activity decreased whereas N- and P-acquiring enzymes showed no significant differences across most plantations; in contrast, subsurface soils exhibited a consistent increase in C-, N-, and P-acquiring enzyme activities. RDA showed that C-, N-, and P-enzymes were mainly influenced by soil microbial biomass and N content. Microbial C limitation was significantly alleviated but P limitation intensified in surface soils, while microbial C and P limitation in subsurface soils showed no significant change across most plantations following conversion. RFA showed that surface C limitation was mainly influenced by microbial biomass stoichiometric ratios, while subsurface C limitation was mainly regulated by NO3- and bulk density. Surface P limitation was primarily driven by soil N content (NH4+, TN and C:N), whereas subsurface P limitation showed no significant driver. These findings highlight introducing native tree species restructures microbial nutrient limitation patterns and functions, underscoring the potential of native species to improve belowground ecological processes in plantation ecosystems and providing mechanistic insights for tree species selection.