Phthalate esters (PAEs) are endocrine disrupting pollutants known to accumulate in various environmental abiotic matrices and biological organisms in global. However, there remains limited understanding of the bioaccumulation and trophic transfer of PAEs within mangrove food webs. This study was based on the MixSimmr model, employing stable carbon and nitrogen isotope tracing, gas chromatography-mass spectrometry (GC-MS) analysis, then systematically assessing the bioaccumulation and trophic transfer of PAEs under natural environmental conditions. Results indicate that Sargassum siliquastrum Sargassum (S.sili.), particulate organic matter (POM), and sedimentary organic matter (SOM) are the primary sources of foundational carbon that support mangrove ecosystems. Aquatic organisms from the mangrove region demonstrated significant bioaccumulation of dimethyl phthalate (DMP) from both water and sediment. Compared to herbivorous and omnivorous fish, benthic carnivorous fish exhibit higher PAEs accumulation. The octanol-water partition coefficient (KOW) value of PAEs was identified as a key factor influencing bioaccumulation. With increasing trophic levels, butyl benzyl phthalate (BBP) and di-(2-ethylhexyl) phthalate (DEHP) exhibited potential biomagnification effects, whereas DMP and diethyl phthalate (DEP) displayed marked trophic dilution. Short-chain PAEs were mainly absorbed by fish through skin and respiration, while long-chain PAEs accumulated via ingestion of SOM and POM. This study offers critical insights into the environmental behavior of PAEs in mangrove wetlands and has significant implications for mangrove wetland ecosystem protection, biological resource management, and risk prevention in aquatic product safety.