The selective culture method and PCR-DGGE technology were applied to analyze the number and the biodiversity of microorganism species in cells with plant intercropping models and without plants in different seasons in a wetland system constructed for treatment of municipal sewage. The results showed that the numbers of microorganisms were considerably larger in the cells with plant intercropping models than those without plants, while the number of microorganisms was apparently larger in summer than that in winter in all treatments. Along the three-sequenced treatment cells with plant intercropping models a "low-high-low" changing trend in the numbers of microorganisms in summer. The UPGMA cluster analysis showed that the treatments in the same season were clustered in the same branch except for a few samples in winter and the biodiversity index was consistently higher in summer than that in winter. Five different sequences (DF1-DF5) were obtained through BLAST analysis and retrieval. The closest known origin groups were located as Escherichia coli, Citrobacter sp., Proteus sp., Klebsiella oxytoca, and Burkholderia sp. respectively. The BLASTX comparison test showed that DF1 closely related to the activities of the Mycobacterium bacillus and the Bacillus amyloliquefaciens, DF2 functioned as a conservative potential ATP binding protein, DF3 related to the activities of the Bacillus cereus spore, DF4 was involved in catabolism metabolism of microorganism and DF5 played an important role in decomposition of organic matters.