[Objective] Farmland soils high in geological background value are widely distributed in China, complex in pedogenesis, and diverse in geological age and parent material. Consequently, by far little is known about mechanisms of their pollution of heavy metals and ecological risks of the pollutants. The purpose of this study was to explore distribution of the heavy metals in paddy soils typical of the karst area of Guangxi, and key factors that affect structures of the microbial communities in the soil, in an attempt to provide certain data support for establishment of a heavy metals risk assessment system for high-geological background-valued farmland soils of the secondary enrichment type. [Method] Samples of four types of paddy soils different in geological age and type of parent material were collected separately in Maling, Luoxu, Suxu, and Yunbiao of Guangxi for analysis of contents and distribution of heavy metals, physical and chemical properties, and the functional diversity of the microbial communities therein. And redundant analysis(RDA)was performed to obtain key environmental factors that impact structures of the soil microbial communities in those soils. [Result] Results show: (1) Development stage and type of parent material significantly affected basic physiochemical properties of the soils, and also concentrations of heavy metals in the soils. The soil in Maling started its development earlier and so was higher in organic matter content and heavy metals enrichment. Derived from carbonate limestone, the soil was also higher in soil Cd than all the other three types of soils derived from Quaternary fluvial sediments; (2) The four types of paddy soils were sharply different in soil microbial activity and microbial community structure. The soil in Suxu was significantly lower in soil microbial carbon source utilization capacity and microbial diversity index than the other three types of soils, where the amine and amino acid utilizing microbes were higher in metabolic activity; However, the soil in Suxu was higher in metabolic activity of the saccharides and polymeric carbon utilizing microbes; (3)RDA shows that soil organic matter, pH, total As, Cd, Pb, and available As were the main environmental factors that caused differentiation of the soil microbes in utilizing carbon sources; and(4)Correlation analysis shows that intensity of the soil microbes utilizing amines, amino acids, and phenolic acids was positively related to soil organic matter and pH, and negatively to As, available Cu, and available As. [Conclusion] For the four types of soils high in geological background value, parent material and geological age are the two factors that determine physical and chemical properties of and distribution of heavy metals in the soil, which then in turn influence community structure and activity of the microorganisms in the soil.