The effects of ZnO nano particles (ZnO NPs) on the composition and diversity of microbial communities in the periodic and long-term submerged areas of coastal wetlands were studied with coastal wetland simulation systems, and the microbes with significant changes were identified by 16S rRNA amplicon sequencing. The results showed the relative abundances and diversities of microbial communities were varyingly affected under the ZnO NPs exposure. ZnO NPs concentration was an important factor that motivated the changes of relative abundances and β diversities of microbial communities in coastal wetland environment. With the increase of the concentration of ZnO NPs, the increased particle size of NPs after agglomeration weakened the impact on microbial community. β diversity was the lowest when the mass concentration of ZnO NPs was 80 mg/L. The influence on microbial community in the periodic submerged area was smaller than that in the long-term submerged area and submerging conditions lead to significantly different bacteria with different classification levels. Different environmental conditions (e.g. dissolved oxygen and organic matter) in periodic submerging area and long-term submerging area led to different effects of ZnO NPs on microbial abundance and community diversity.