Soil microorganism activity in an agricultural field is affected by various factors including climate conditions, soil chemical properties, and crop cultivation. In this study, we elucidate the correlation between microorganism activity and agricultural environment factors using the dehydrogenase activity (DHA) value, which is one of the indicators of soil microbial activity. As a result, the various factors noted above were related to the DHA value. Annual rainfall, soil Mg2+, bacterial and fungal diversities, types of crops, developmental stages, seasons, and cultivation status were highly correlated with the DHA value. Furthermore, next-generation sequencing (NGS) analysis was used to identify that the type of crop affected soil microbial compositions of both bacteria and fungi. Soil used for soybean cultivation showed the highest relative abundance for Verrucomicrobia, Planctomycetes, and Acidobacteria but Actinobacteria and Firmicutes had the lowest relative abundance. In the case of soil used for potato cultivation, Actinobacteria had the highest relative abundance but Proteobacteria had the lowest relative abundance. Armatimonadetes showed the highest relative abundance in soil used for cabbage cultivation. Among the fungal communities, Mortierellomycota had the highest relative abundance for soybean cultivation but the lowest relative abundance for cabbage cultivation; further, Rozellomycota, Chytridiomycota, and Cercozoa had the highest relative abundance for cabbage cultivation. Basidiomycota had the highest relative abundance for potato cultivation but the lowest relative abundance for soybean cultivation.