The soil microorganisms at different depths play an important role in soil formation, ecosystem biogeochemistry, recycling of nutrients, and degradation of waste products. The aims of this study were to observe the microbial diversity in the profile of an agricultural soil in North China, and to research the correlation between soil microbes and geochemistry. First, the soil geochemistry of the profile was investigated through 25 chemical elements. Secondly, the various physiological groups of microorganisms were studied by traditional culture methods. Thirdly, the functional diversity on sole carbon source utilization (SCSU) was evaluated by the BIOLOG(r) system. Finally, the correlation between the soil microbial diversity and geochemistry was analyzed statistically. The results showed that the amounts and proportions of various physiological groups of microorganisms changed with depth. The bacterial functional diversity on SCSU decreased with increasing depth, but evenness of the substrate utilization increased. Although the microbial metabolic diversity was different at every depth, it could be classified into three main grous by principal component analysis and cluster analysis. The various physiological groups of microorganisms showed remarkable correlation with relevant soil chemical elements. The sensitive microbial indicators of soil health were expected to be screened out from actinomyces or ammonifying bacteria.