Continuous cropping of soybean causes soil degradation and soybean yield decline, but these effects could be alleviated by crop rotation or the use of long-term continuously cropped soybean systems. However, the mechanism by which biotic and abiotic factors are affected by different cropping systems remain unclear. In this study, we comparatively investigated the bacterial and fungal abundance, diversity and community compositions in the bulk and rhizospheric soils of soybean continuously cropped in the short-term for 3 and 5 years (CC3 and CC5) and in the long-term for 13 years (CC13), as well as cropping rotation with maize in alternately for 5 years (CR5) using qPCR and high-throughput sequencing methods. The results showed that soil pH, and available nutrients such as N, P and K were significantly higher in the bulk soils of CC13 and CR in contrast to CC3 and CC5. The fungi/bacteria ratio was significantly higher in the rhizospheric soils of CC3 and CC5 than that in CR5 and CC13, indicating that short-term continuously cropped soybean decreases bacterial abundance but increases fungal abundance. The bacterial and fungal community structures were significantly altered by different cropping systems, and the soil pH and C/N were the primary soil factors in shifting the bacterial and fungal community structures in the bulk soils, respectively. Bacterial and fungal co-occurrence patterns were remarkably affected by cropping systems, which showed that CC13 and CR5 harbor co-occurrence networks that are more complex than CC3 and CC5. Moreover, CC13 and CR5 increased the relative abundances of potentially beneficial bacteria Bradyrhizobium sp. and Gemmatimonas sp. and fungi Mortierella sp. and Paecilomyces sp. but decreased the relative abundances of the pathogenic fungi Fusarium sp. in contrast to CC3 and CC5, which indicated that long-term continuous cropping of soybean might have generated a possibility of the development of disease-suppressive soils.