To achieve the coordinated development of rational marine resource allocation and environmental protection, marine functional zoning divides coastal areas into different functional zones, resulting in varying levels of human activity pressure across these zones. Scientific assessment of ecological quality differences among different marine functional zones is essential for the sustainable utilization of marine spatial resources. The study conducted a survey on the macrobenthos communities in the port zone, marine protection zone, fishery zone, and shipping zone of the sea area adjacent to the Yalujiang Estuary from 2020 to 2022. Based on the taxonomic and functional traits of macrobenthos, an ecological quality assessment system for the Benthic Index of Biotic Integrity (B-IBI) was constructed. A total of 139 macrobenthos species were identified, including 63 annelids, 39 arthropods, 22 mollusks, 6 echinoderms, 3 chordates, and 6 species of other taxa. The taxonomic and functional traits of macrobenthos exhibit differences among different marine functional zones. The port zone mainly exhibited community characteristics of tolerant taxa, including a higher proportion of polychaetes, second order opportunistic species, deposit feeders and tube dwellers. The marine protection, fishery, and shipping zones exhibited characteristics of communities dominated by sensitive taxa, including high proportions of mollusks, small and medium sized species, plankton feeders, free living species, and swimmers. From 41 candidate indicators based on taxonomic and functional traits, six core indicators were selected through distribution range analysis, discriminative capacity evaluation, and redundancy assessment for B-IBI model construction. The assessment results showed that the overall ecological quality of the sea area adjacent to the Yalujiang Estuary was good and showed a trend of increasing from the port zone to other marine functional zones. Except for the port zone, which exhibited poor ecological quality, the marine protection, fishery, and shipping zones all maintained good ecological quality, suggesting that the port zone may be under stress from human activities such as land-based pollution and port operations. Correlation analysis showed that B-IBI was significantly negatively correlated with pollution factors such as NO₃^--N, NH₄⁺-N, PO₄^3--P, and Hg, suggesting that it reflected the impacts of riverine input and aquaculture sewage discharge on the estuary's ecological quality. This study confirmed the effectiveness of B-IBI in assessing the ecological quality of different marine functional zones in the Yalujiang Estuary. It effectively reflected the differences in ecological quality among marine functional zones under the stress of pollutants, thus providing a basis for the assessment of marine functional zoning.