affecting the initiation and dissipation of Microcystis blooms. Nutrients represent a key factor driving microbial growth, and fluctuations in nutrient levels frequently accompany Microcystis bloom cycles. To explore how nutrient variations shape the bacterial communities associated with Microcystis colonies, this study employed a non-axenic strain of colonial Microcystis aeruginosa isolated from Lake Taihu as the model system. Through a multi-nutrient gradient culture experiment, the effects of different nutrient regimes—including nitrogen-deficient (ND), oligotrophic (O), mesotrophic (M), eutrophic (E), and highly eutrophic (BG-11) conditions—were evaluated, and the responses of the associated bacterial communities to nutrient fluctuations during Microcystis growth were analyzed. Results demonstrate that nutrient concentration significantly modulates bacterial community composition and alpha-diversity. Communities under ND, O, and M conditions exhibited greater similarity to each other, whereas those under E and BG-11 conditions diverged more markedly. Elevated nitrogen and phosphorus levels were associated with reduced community richness and diversity. Core bacterial phyla included Proteobacteria, Bacteroidota, and Armatimonadota, with dominant orders such as Rhizobiales, Caulobacterales, and Pseudomonadales. Core taxa varied across nutrient regimes: the BG-11 group was characterized by Actinobacteria and Cytophagales; the O group featured Bradyrhizobiaceae and Hyphomicrobiaceae; the ND group was dominated by Rhizobiales; and the M group showed prominence of Comamonadaceae, underscoring nutrient-driven shifts in the Microcystis-associated bacteriome. Furthermore, nutrient gradients influenced community stability and interaction patterns: under eutrophic conditions, Microcystis displayed stronger resistance and responsiveness, while bacterial cooperation prevailed in oligotrophic settings, shifting toward competitive interactions under nutrient enrichment. This study elucidates how nutrient gradients regulate algal–bacterial interactions and associated microbial community assembly, offering mechanistic insights into the persistence of Microcystis blooms across trophic gradients.