With pot experiment, this paper studied the quantitative variations of bacteria, actinomyces, mould and yeast in soils of peanut intercropped with medicinal plants, aimed to test if such an intercropping pattern could remove the obstacles of peanut's continuous cropping. The results showed that Atractylodes lancea and Euphorbia pekinensis had the strongest inhibitory effect on mould. Compared with CK (mono-cropping peanut), the CFU of mould in the treatments intercropped with A. lancea and E. pekinensis was decreased by 53.87% and 29.59%, respectively during flowering-pegging stage of peanut, but increased after harvesting, which was in favor of substance circulation and nutrient returning. The CFU of bacteria in treatments intercropped with A. lancea, E. pekinensis and Pinellia ternate was all increased, and that of yeast in all five intercropping treatments was increased during the flowering-pegging stage of peanut. No familiar pathogens were found in the treatments intercropped with A. lancea, E. pekinensis and Diosoren zingiberebsis. Peanut intercropped with medicinal plants could regulate soil microbial community effectively.