Sediment microbial communities are responsible for many chemical biotransformation processes in the aquatic environment and play a critical role in various ecosystems and biogeochemical cycling. However, the impact of polyfluoroalkyl substances on sediment microbial communities remains unclear. These substances are increasingly being used in consumer and industrial products to replace environmentally persistent perfluoroalkyl substances. In this study, we investigated the effects of low (5mg/L) and high (15mg/L) doses of 6:2 fluorotelomer alcohol [6:2 FTOH, F(CF2)6CH2CH2OH] on the structure of a sediment microbial community. 6:2 FTOH biotransformation was rapid in the sediment mixture with a half-life <3days, regardless of the initial doses. After 28days, major products produced in the high dose condition included 28mol% 5:2 sFTOH [F(CF2)5CH(OH)CH3], 9.6mol% 5:3 Acid [F(CF2)5CH2CH2COOH] and 11mol% PFHxA [F(CF2)5COOH], while 73mol% 5:2 sFTOH, 23mol% 5:3 Acid and 26mol% PFHxA were observed in the low dose condition. In the original (control) sediment without 6:2 FTOH dosing, Proteobacteria was the predominant microorganism (18%), followed by Chloroflexi (14%), Verrucomicrobia (13%), Firmicutes (3.4%), Bacterioidetes (2.4%), Actinobacteria (1.7%) and Planctomycetes (1.3%). The presence of 6:2 FTOH and the accumulation of transient transformation products in the sediment exerted selection pressure on the microbial taxonomic distribution and diversity. Our observations indicate that potential 6:2 FTOH degraders and tolerant strains, such as Dokdonella spp., Thauera spp., Albidovulum spp. and Caldanaerovirga spp., existed in the sediment mixture and began to dominate over time. This suggests that these genera might have higher tolerance towards elevated 6:2 FTOH and its transformation products. These findings on the characterization of sediment microbial community stability and dynamics will help predict changes in response to perfluoroalkyl and polyfluoroalkyl substances and also help identify robust microbial strains to degrade polyfluoroalkyl substances in the environment.