The Jiulongjiang Estuary, located between the eastern coastal waters of Zhangzhou City and the western coastal waters of Xiamen City, features a broad salinity range (1.8‰—28.2‰) and is subject to frequent shipping and fishery activities. In 2022, quarterly survey were conducted at eight stations to investigate macro-benthic faunal diversity, distribution patterns, and influencing factors within this estuarine area. A total of 101 macro-benthic faunal taxa were identified, averaging a density of 376.3 ind./m² and a wet biomass of 4.92 g/m², predominantly consisting of species with small body sizes. The dominant species common across the mixing zone (E1—E4) and marine zone (E5—E8) were Corophium sp., Mediomastus sp., and Gammarus gregoryi. A one-way ANOVA revealed significant differences in the Shannon-Wiener diversity index (H'), Margalef richness index (D), and Pielou evenness index (J') among stations. Mantel analysis indicated that polychaete communities were significantly influenced by phosphorus-related parameters (phosphate [PO₄^3-], total particulate phosphorus [TPP], total phosphorus [TP]) and cyanobacteria biomass. Pearson correlation analysis showed that macro-benthic faunal diversity was inversely correlated with nitrogen parameters (nitrite-N [NO₂^--N], nitrate-N [NO₃^--N], dissolved inorganic nitrogen [DIN]) and phosphorus parameters (TP, total dissolved phosphorus [TDP], TPP) while showing positive correlations with salinity, conductivity, and total dissolved solids (TDS). The random forest model identified TDP as the primary factor influencing macro-benthic faunal diversity. Significant seasonal differences were also observed in macro-benthic faunal community composition. Overall, the diversity patterns of macro-benthic fauna were jointly regulated by salinity, nitrogen, and phosphorus, with potential disturbances at certain stations linked to hydrodynamic conditions, substrate types, and construction activities. Long-term monitoring in the Jiulongjiang Estuary is necessary to clarify further the driving factors of macro-benthic faunal diversity patterns.