With mounting demand for high-quality agricultural products and the relentless exploitation of arable land resources, finding sustainable ways to safely cultivate food crops is becoming ever more important. Here, we investigated the effects of the integrated cropping technique “straw return + intercropping” on the soil aggregates as well as the microbial biomass carbon (MBC) content, enzyme activities and microbial diversity in soils of maize and soybean crops. Our results show that in comparison to straw removal and monoculture, straw return and intercropping increase the rhizosphere’s MBC content (59.10%) of soil, along with urease (47.82%), sucrase (57.14%), catalase (16.14%) and acid phosphatase (40.66%) activities as well as the microbial diversity under maize and soybean. Under the same straw treatment, the yield of maize when intercropped surpassed that when grown in monoculture, with the land equivalent ratio of the intercropping treatment under straw return being highest. Overall, the intercropping of maize and soybean is beneficial for the healthy development of sustainable agriculture in the black soil region of northeast China, especially when combined with straw return to fields.