Daya Bay, a typical semi-enclosed bay in the South China Sea, has experienced long-term nutrient accumulation. In recent years, it has become a hot  research area owing to its high phycotoxin levels. Toxin production by harmful algae is a complex process regulated by multiple interacting factors. However, most of studies have focused on individual toxins or algal species, leaving the interactive effects among environmental factors, diverse toxigenic algae, and microbial communities largely underexplored. In this study, a systematic seasonal survey was conducted in Daya Bay across four seasons of 2024. By integrating environmental parameters, intracellular and extracellular phycotoxins, high-throughput sequencing, and multivariate statistical analyses, we established an integrative analytical framework linking environmental factors, microbes, toxigenic algae, and diverse phycotoxins.Our results showed that diatoms were the dominant phytoplankton group throughout the year (approximately 45%), while dinoflagellates exhibited relatively low abundance. Toxigenic algae were primarily represented by Pseudo-nitzschia and Gymnodinium.All phycotoxins exhibited a consistent spatiotemporal pattern, with higher concentrations in summer and autumn, lower levels in winter and spring, and a decreasing gradient from the inner bay to the outer bay. Domoic acid (DA) was the predominant toxin component, reaching a maximum concentration of 661 ng·L^-1.Different phycotoxins were regulated by distinct environmental drivers: DA showed strong positive correlations with high temperature, high chlorophyll a concentration, and low salinity; the accumulation of dinophysistoxin (DTX1) and yessotoxin (YTX) was significantly negatively correlated with dissolved inorganic nitrogen (DIN) consumption; spirolides (SPX) and gymnodimines (GYM) were positively correlated with N:P ratio imbalance; while saxitoxin (STX) and pectenotoxin (PTX2) co-varied with elevated salinity and nitrite levels.Microbial co-occurrence network analysis revealed that phytoplankton-microbial communities exhibited significantly higher network stability than free-living microbes. During seasons with high toxin concentrations, the internal connectivity among phytoplankton-microbes decreased, whereas their connectivity with toxigenic algae increased. Rhodobacteraceae and Flavobacteriaceae were identified as core microbes. Metagenomic functional annotation indicated that both families were enriched in carbon and nitrogen metabolic pathways, suggesting their potential involvement in nutrient remineralization, thereby modulating algal growth and toxin production.Collectively, this study elucidates the interactions among diverse toxigenic algae, environmental factors, and microbial communities in Daya Bay, and establishes an environment-microbes coupling framework for multi-toxin co-variation.These findings provide a scientific foundation for refined ecological risk monitoring in complex phycotoxins profiles.