Via field experiments, the different effects of inorganic biological material hydroxyapatite and the combined remediations of three kind of plants (Elsholtzia Splendens, Pennisetumsp, Sedum plumbizincicola) with hydroxyapatite on the absorption of soil total Cu and Cd, the passivation and absorptive ability for available Cu amd Cd derived from Cu and Cd contaminated soils in Guixi was compared. PLFA method was used to study the effects of different remediations on soil microbial community, aiming to assess the response of soil micro-ecological environment to various remediations. The results showed that the application of hydroxyapatite increased soil pH value significantly and passivate available Cu and Cd in soil, while had little influence on total Cu and Cd contents in soil. The combined remediations of plants and hydroxyapatite not only reduced soil available Cu and Cd significantly (P<0.05), but also decreased soil total Cu and Cd contents in plant rhizosphere (P<0.05), mainly due to plant tissues absorption and fixation for metals, particularly the aboveground fractions. The effects of different remediations were significantly different on the composition of soil microbial community, sole hydroxyapatite application was positively correlated with soil fungi community and increased soil fungi biomass, which increased fungi/bacteria ratio, while the combined remediation of plant and hydroxyapatite could alleviate the trend of soil fungi enrichment effectively, the combined remediation of Pennisetumsp and hydroxyapatite increased the biomass and diversity of soil Gram positive and Gram negative bacteria and decreased F/B ratio, thus reduced the risk of soil fungi diseases. In addition, organic matter accumulation caused by different plants root metabolism significantly improved rhizosphere organic C of the combined remediation treatments. ABT analysis indicated that different remediations were most important influential factor on soil microbial community, other factors included soil pH value, the content and availability of Cu. The above results explained the combined remediation of plant and hydroxyapatite on soil micro-ecosystem from the perspective of microbial community composition, thus can provide reliable theory bases for the screening and conducting of combined remediation of plant and inorganic biological materials in Cu and Cd contaminated regions.