Cover cropping in orchard systems is an efficient approach to enhance soil available phosphorus (P). However, the impact of legume species on available P and P fractions, as well as the microbial response to legume cover cropping in karst mango orchard soil in China, is not well understood. To elucidate these unknowns, the responses of soil P availability, P fractions, and phoD-harboring microbial communities in karst areas to the cover cropping of three legume species (Desmodium intortum (DI), Chamaecrista rotundifolia (CR), and Vicia villosa Roth (VR)) in mango orchard soils in a karst region were investigated using conventional clear tillage as the control. In the 0–10 cm soil layer, legume cover crops led to significant rise in total P, labile-P (i.e., Resin-P and NaHPO₃-P_i), and moderate-P (NaOH-P_o) fractions, potentially increasing the supply of soil P. Among the three cover crops, only the CR treatment resulted in a significant rise (P < 0.05) in the soil available P. In the 10–20 cm soil layer, most of the labile-P fractions did not increase with legume cover crops. The biomass of bacteria, fungi, Actinomycetes, and arbuscular mycorrhizal fungi increased in mango orchard soil with legume crops. Legume cover crops significantly improved the richness of phoD-harboring bacteria and fungi (P < 0.05) and promoted the growth of specific P-solubilizing bacteria, which facilitated P fraction transformation by soil phosphatase. Moreover, the increased co-presence of phoD-harboring bacterial and fungal networks was observed after legume cover cropping. Redundancy analysis indicated that increases in total nitrogen, phosphodiesterase activity, and P-solubilizing bacteria (such as Bradyrhizobium) are important drivers of soil P availability. Collectively, the results indicate that in karst areas, legume cover crops in mango orchards can promote soil P cycling, and that planting C. rotundifolia in particular can effectively improve soil P availability.