Intensive agriculture with continuous monocropping and massive chemical inputs has adversely affected belowground microbial composition and functions, resulting in soil sickness and negative feedbacks to crop growth and production. Crop diversification has been highlighted to address these problems in a more sustainable and ecological way by alterations of the temporal and spatial interactions between above- and belowground biota. However, the underlying mechanisms of crop diversity in alleviating monoculture soil sickness remain elusive. Here we propose that soil microbial networks could be a key entry point to understand the intercropping benefits on soil fertility and pathogen or pest control. Last, we raise some promising directions facing future challenges which might be beneficial to future agricultural managements and food security, and how to design an optimized cropping system to construct a healthier soil.