Non-native plants can significantly affect biodiversity and ecological functions of local ecosystems. The effects of Kandelia obovata introduction and Spartina alterniflora invasion on benthic bacterial communities, predicted ecological functions and interactions between macrobenthos and microorganisms were studied. High-throughput sequencing of the 16S rRNA gene was used to investigate the bacterial communities in sediments covered by S. alterniflora and K. obovata at different stand ages. Bacterial communities showed obvious spatial variation. With increasing in planting age, K. obovate sediments were occupied by higher proportions of bacteria involved in degradation of organic carbon compounds, including various sulfate reduction bacteria, Bacteroidetes, Alphaproteobacteria, and pathogenic bacteria Vibrio, while the relative abundances of Actinomatinales and Sulfurovum were more abundant in younger K. obovate sites. Compared to adjacent mudflat, higher abundances of sulfate reduction bacteria were observed in S. alterniflora. This study indicated that K. obovata introduction had greater effects on bacterial communities, and sediment pH, grain size, soil organic carbon, total nitrogen and total phosphorus contents were main environmental factors affecting variation in bacterial communities. Tax4fun analysis further suggested that higher potentials of nitrogen fixation and dissimilatory sulfate reduction were observed after K. obovata restoration and S. alterniflora invasion. There were significant correlations between macrobenthos and bacterial communities, especially variations in relative abundance of infaunas and herbivores after K. obovata introduction and S. alterniflora invasion, which significantly affected bacterial communities and potentials involved in nitrogen cycling. The present study provided valuable information in scientific assessing the impacts of non-native plant disturbance on local ecosystems.