Ulva prolifera green tide is a serious marine ecological problem in China's coastal areas, with recurrent outbreaks occurring annually during late spring and summer since 2007. Marine bacteria communities are closely linked with important ecological functions in coastal environments. Hence, the succession of bacterial community structures in seawater and sediments during the outbreak and extinction stages of U. prolifera green tide were studied in this paper. The results revealed that: (1) the outbreak of a green tide led to changes in the bacterial community structure and a reduction in the abundance and diversity of the bacterial community in the Qingdao offshore region. This change was more significant in sediments than in seawater. (2) The bacterial assemblage appeared to be dominated by members of Deltaproteobacteria, Bacteroidia and Flavobacteria in sediment, and reductions in the relative abundance of Flavobacteria and Alphaproteobacteria were also observed in seawater after the green tide outbreak. There was also a high similarity in species composition of bacteria in sediment (extinction stage) and seawater (outbreak stage). (3) The outbreak of the U. prolifera affected the abundance of functional bacterial communities in the offshore environment such as SRB (sulfate-reducing bacteria), CFB (Cytophaga-Flavobacter-Bacteroides), heterotrophic bacteria and the potentially algicidal bacteria Alteromonadaceae. Overall, U. prolifera affects aquatic ecosystem secondary production, biogenic geochemical cycles and the growth of other seaweeds in Qingdao offshore areas by driving variations in functional bacterial communities.