As the main component of marine endogenous dissolved organic matter, algae-derived dissolved organic matter (A-DOM) is released into seawater by phytoplankton during the growth and death decomposition period. Polybrominated diphenyl ethers (PBDEs) are widespread in marine ecosystems, despite the restrictions imposed on several congeners, and pose a threat to marine organisms. Many coexisting factors, especially DOM, affect the environmental behavior and ecological risk of PBDEs. However, the interaction pattern and mechanism between marine A-DOM and PBDEs remains unknown. Since blooms frequently occur in coastal waters, Skeletonem costatum was selected as the source of A-DOM and examined the interaction of A-DOM with 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47). In addition, their combined effects on biological toxicity of typical marine zooplankton Brachionus plicatilis were analyzed, and the potential mechanisms were discussed. The results showed that A-DOM fluorescence was statically quenched by BDE-47. The functional groups such as amide, carbonyl and hydroxyl in A-DOM involve in the interaction between A-DOM and BDE-47. Molecular docking results demonstrate that proteins in A-DOM could spontaneously bind with BDE-47 and that hydrophobic interactions, van der Waals forces and pi-bond interactions existed. Compared to BDE-47 treatment, the reproductive toxicity, oxidative damage and inhibition of mitochondrial activity induced by BDE-47 in rotifers were alleviated by A-DOM addition. Transcriptomic analysis further showed that A-DOM could exhibit the potential to mitigate the biotoxicity of BDE-47 by activating the energy metabolism pathway, alleviating DNA damage and upregulating genes encoding metabolic detoxification proteins. This study reveals the complex role of marine A-DOM in BDE-47 bioavailability and enhances the knowledge related to risk assessments of PBDE-like contaminants in marine environments. It would be significant to evaluate the interactions of various types of pollutants with A-DOM while extrapolating these findings to natural aquatic environments.