An investigation was conducted by using fatty acid methyl ester (FAME) profiles to follow the spatial response of the microbial community at 2 mm scale with the purpose of illustrating the mechanism of nonlinear spatial dependence of pyrene degradation on the distance from the root surface in the rhizosphere of maize seedlings (Zea mays L.). The soil in the rhizobox was divided into several compartments separated by nylon meshes. Soil samples were collected from the root compartment (S0) and other compartments of 0-2 mm (S1), 2-4 mm (S2), 4-6 mm (S3), ＞6 mm (S4) far from the root compartment to determine extractable pyrene concentrations and fatty acid methyl ester. Zea mays L. was grown in environmental chambers for 45 days with soil spiked with 600 mg/kg pyrene. The results showed that significant differences existed between the compartments in extractable pyrene concentrations in treatments with maize, following the order of S4＞S3＞S0＞S2＞S1. However, an opposite trend in variation existed with fatty acid indicators of soil microbial biomass and of arbuscular mycorrhizal fungi (AMF). Significant differences existed among the compartments in microbial community structure in treatments with maize. No difference existed in extractable pyrene concentration and microbial community structure between treatments without maize. Significantly negative correlations (p<0.01) existed between the extractable pyrene concentrations and fatty acid indicators for microbial biomass and fatty acid indicators for AMF in various sampling zones of soils with growth of maize.