Monoculture and rotation systems usually exhibit distinct diversity and composition of microbial community in the cultivation of various plants, but the network structures and keystone species of microbial communities in these two cropping systems are poorly understood. To better understand this issue, we constructed four ecological networks of bacterial communities in bulk and rhizosphere soils of soybean grown in the two cropping systems, i.e. continuous cropping of soybean (CC) and acropping rotation with maize (CR), using Molecular Ecological Network Analysis Pipeline (MENAP). The results revealed that the bacterial network structure and composition between the two cropping systems in both bulk and rhizosphere soils were greatly different, with larger differences between CC and CR in rhizosphere soils than in bulk soils. Compared with CC, CR increased the stability and complexity of bacterial networks in both bulk and rhizosphere soils. Predominantly positive (> 75%) correlations in all the networks indicated that extensive cooperative interactions occurred among bacterial taxa in Mollisols. Putative keystone species that typically had low relative abundance performed distinct ecological functions in the two cropping systems. These results provide new insights into the bacterial interactions and ecological function in continuous cropping and crop rotation systems.