Soil microbes play an important role in nutrient cycling, and their richness and diversity are greatly influenced by cropping patterns and soil management systems. However, the effect of different cropping systems of rice on soil microorganism is still obscure. Therefore, this field experiment was conducted to study the effects of various paddy-upland multiple cropping rotation patterns on soil microbial community structure and diversity. The experiment comprised different treatments, Chinese milk vetch (Astragalus sinicus L.)-double cropping rice (CRR, CK), rape-early rice-late rice (RRR), potato (Solanum tuberosum L.)-early rice-late rice (PRR), Chinese milk vetch-early rice-sweet potato (Ipomoea batatas (L.) Lam.) late soybean (Glycine max (L.) Merr.) (CRI), and rape (Brassica napus L.)-early rice-sweet potato late soybean (RRI). The results showed that rapeseed and Chinese milk vetch in winter was conducive to increasing bacterial community richness and diversity. For each cropping pattern, the top three dominant phyla in paddy fields were Proteobacteria, Chloroflexi and Actinobacteria in terms of relative abundance. The community structure of soil bacteria showed more significant internal variability in CRI and RRI treatments and less internal variability in others treatments. Redundancy analysis of soil bacterial community structure and soil chemical properties revealed that soil bacterial community structure changes were primarily influenced by organic C, its fractions, and N content. In conclusion, Chinese milk vetch-early rice-sweet potato and late soybean cropping patterns may be considered for sustainable early and late rice production due to their beneficial impacts on soil bacterial abundance, diversity, and soil properties.