A paddy-upland crop rotation field experiment, consisting of 5 treatments, i.e. fallow-rice (CK), rape-rice (R-R), corn-rice (C-R), milk vetch-rice (M-R) and bean-rice (B-R), was conducted to investigate effects of the rotation modes on bacterial community structure in cold waterlogged paddy soil, using the high-throughput sequencing technique, and relationship between soil physicochemical properties and bacterial community structure as well. Results show that compared with CK, paddy-upland rotation significantly increased rice yield by 18%~44%, but decreased richness of the soil bacterial community in most cases. However, the rotation did not affect much bacterial diversity. Proteobacteria and Acidobacteira were dominant bacterial groups in all the soil samples, and Proteobacteria was the highest in relative abundance. Compared with CK, rotation significantly increased relative abundances of Acidobacteria, Actinobacteria, Nitrospirae, Bradyrhizobium and Nitrosospira and various bacterial groups involved in carbon and nitrogen recycling. Cluster analysis shows that CK and M-R belonged to a group, B-R, C-R and R-R to the other group in terms of soil bacterial community. Redundancy analysis demonstrates that soil total phosphorous, available phosphorous and pH were the main factors affecting soil bacterial community structure.