Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are special components of bacterial membrane lipids and are ubiquitously found in diverse terrestrial and marine environments. Acidobacteria have been recently evidenced as one of their source microorganisms in terrigenous environments, such as acidic soils and peats. However, the biological sources of brGDGTs, their distributions and ecophysiological responses, and these biotic impacts on the relationships between brGDGT-based proxies and environmental variables (e.g., ambient temperature, pH, and dissolved oxygen content) in the marine realm are poorly understood. In this study, we analyzed C5- and C6-methylated brGDGTs as well as bacterial communities in the surface sediment samples from the Yangtze River Estuary (YRE) to the East China Sea (ECS), aiming to explore the relationship between brGDGT distribution and bacterial composition and to examine how benthic conditions and bacterial communities jointly influence the spatial patterns of brGDGTs from marine sediments. Substantial differences in the spatial distribution of brGDGTs from coast to shelf were observed. The increase in the proportion of brGDGTs with cyclopentyl and C6-methyl moieties (e.g., Ic and IIc’) and #ringstetra values of >0.7 indicate the occurrence of marine-sourced brGDGTs in the shelf. Statistical analyses suggest that the bacterial community structure and the geochemical and environmental variables may contribute 43.56% and 29.97% to the brGDGT distribution, respectively. Multiple significant correlations between bacterial groups at the order level and brGDGT compounds suggest that bacteria such as Gemmatimonadetes, Planctomycetes and Proteobacteria may potentially contribute to the brGDGT production in marine environments. With the consideration of benthic environmental changes, the shift in bacterial community structure could further result in the variations of brGDGT-based proxies incorporating cyclopentyl and C6-methyl moieties that are likely to be produced by benthic marine bacteria. Overall, in addition to environmental conditions of the ocean bottom, the potential influence of bacterial community structure on the distribution of brGDGTs highlights the caution of using brGDGT-based proxies as terrestrial indicators in coastal oceans.