The occurrence and distribution characteristics of tetrabromobisphenol A (TBBPA) and its relationship with microbial community diversity in different mangrove sediments need further investigation. The results of this study indicated levels of TBBPA in mangrove sediments from the Zhangjiang Estuary (ZJ), Jiulongjiang Estuary (JLJ), and Quanzhou Bay (QZ) in Southeast China ranging from 1.80 to 20.46, 3.47 to 40.77, and 2.37 to 19.83 ng/g dry weight (dw), respectively. Mangrove sediments from JLJ contained higher levels of TBBPA, possibly due to agricultural pollution. A correlation analysis revealed a significant correlation between total organic carbon (TOC), total nitrogen (TN), and TBBPA distribution in ZJ and JLJ mangrove sediments, but not in QZ mangrove sediments. TOC significantly affected the distribution of TBBPA in mangrove sediments, but pH had no effect. High-throughput 16S rRNA gene sequencing showed that Pseudomonadota dominated the sediment bacteria followed by Chloroflexota, Actinobacteota, Bacillota, Acidobacteriota, Bacteroidota, and Aminicenantes in mangrove sediments. Although the microbial community structure of the ZJ, JLJ, and QZ mangrove sediments was similar, the taxonomic profile of their sensitive responders differed markedly. The genus Anaerolinea was dominant in the mangrove sediments and was responsible for the in situ dissipation of TBBPA. Based on redundancy analysis, there was a correlation between TBBPA, TOC, TN, C/N, pH, and microbial community structure at the genus level. Combining TBBPA, TN, and TOC may induce variations in the microbial community of mangrove sediments.