Soybean[Glycine max (L.) Merill.] continuous cropping may lead to yield decline, enriched pathogenic microbes, and soil degradation. Although the problems can become serious, the mechanisms of how the bacterial community is affected and possible links between these effects and cropping systems remain unclear. Therefore, we comparatively investigated the bacterial diversity and structure of the soil samples collected from soybean continuous cropping with different years (CC-) and cropping rotation with maize (CR) using Illumina Miseq sequencing methods. The results showed that soil pH, total N, total P, and available nutrient content were significantly higher in CR5 and CC13 treatments. Compared with short-term continuous cropping, CR5 and CC13 treatments increased the number of OTUs (operational taxonomic units), value of PD (phylogenetic diversity), Chao1 index, and Shannon index of bacterial communities. The cluster analysis revealed that the bacterial community compositions were affected both by the cropping system and cropping years, and soil pH, TN (total N), TP (total P), AN (available N), AP (available P), and AK (available K) were the main factors in driving bacterial community structure (P < 0.05). In addition, a variance partitioning analysis (VPA) revealed that the effect of soil pH was a primary factor in determining bacterial community composition. In this study, the results showed that soil nutrient content and richness and diversity index of the bacterial community increased under CC13 treatments, which indicated that long-term soybean continuous cropping improved the soil environment to some extent. This study provides scientific data for studying the ecology of soybean continuous cropping.