The multiple cropping index of the land in the Huang-huai-hai area is high, and there are no leisure conditions, resulting in serious consumption of soil nutrients and a decline in the diversity of soil microbial communities. In order to improve soil conditions, based on a two-year maize-legume cover crops (alfalfa, soybean, peanut) intercropping experiment, this study is to explore the effects of maize legume cover crops intercropping on soil nutrients, soil enzyme activities and fungal community characteristics, and to analyze the feasibility of intercropping maize and legume cover crops in the fluvo-aquic soil area of ​​Huang-huai-hai Plain. The results showed that soil available nitrogen increased and soil organic matter did not change significantly. under intercropping conditions, soil available phosphorus of maize-alfalfa intercropping treatment and maize-peanut intercropping treatment showed an upward trend. Soil urease activities of all intercropping treatments were higher than that of monocropping treatment. Acid phosphatase activities of intercropping peanut treatment and intercropping soybean treatment increased by 30.53% and 18.70% respectively compared with monocropping; the activities of soil alkaline protease and sucrose of intercropping alfalfa treatment enzyme activity were significantly improved compared with single crop maize. Intercropping alfalfa treatment and intercropping soybean treatment had positive effects on the relative abundance of soil dominant phylum Ascomycota and Mortierella. Among them, intercropping alfalfa treatment increased the relative abundance of Ascomycota by 11.88%, while intercropping soybean treatment increased the relative abundance of Mortierella by 45.39%. The increase in the abundance of the dominant bacteria phyla can help supplement soil nitrogen and carbon sources. Intercropping of maize and legume cover crops can supplement soil nutrients, improve soil microbial community structure, and increase soil enzyme activities, thus, it may be an effective measure to improve soil quality and maintain soil stability in the Huang-huai-hai Plain.