Excessive reclamation leads to rapid degradation of wetland ecosystems. Microbial changes in wetland soils under the influence of human activities can sensitively indicate degradation of soil quality and ecosystem functions. To study the effects of different land use patterns on microbial community structure of wetlands, the Sanjiang Wetland Protected Area of Fuyuan, Heilongjiang Province, was selected as the research area. Soil samples were collected from replanting legume crop area, rice wetland, and primitive peat wetland. Then, the bacterial community structure in the soil was investigated with high-throughput sequencing based on the 16S rRNA gene. The relationship between bacterial community and environmental factors was further explored. The results indicated that, based on the bacterial phylum, there are no significant differences between the microbial community structures of soils under different land use patterns. Nevertheless, at the genus level, higher abundance of Blastocatella, Coxiella, and Rickettsia were detected in the legume rhizospheric soil. In the paddy soil, the relative abundances of Massilia, Nitrosomonas, and Bradyrhizobium are higher, while in the peatand soil, the higher contents are of Rhizomicrobium, Arthrobacter, and Bacillus. The results of Chao1 and Shannon index indicate that the microbial diversity of the paddy soil was higher than in the legume rhizospheric soil and peatland soils. However, no significant differences on bacterial diversity between the legume rhizospheric soil and peatland soils were observed. The results of the correlation analysis indicate that soil reclamation triggers a shift in microbial community mainly because of its influence on soil pH, moisture, and nutrients.