Harmful cyanobacterial blooms have been a global environmental problem. Discharge of anthropogenic pollutants and excess nutrient import into the freshwater bodies may be the biggest drivers of bloom. Bisphenol A (BPA), a typical endocrine-disrupting compound, is frequently detected in different natural waters, which was a threat to the balance of aquatic ecosystem. Yet mechanistic understanding of the bloom and microcystin generation under combined pollution conditions is still a mystery. Herein, the cellular and metabolomic responses to BPA exposure and phosphorus (P) levels in Microcystis aeruginosa were investigated throughout its growth period. The results showed that the stress response of M. aeruginosa to BPA was characterized by a decrease in growth density, an increase in P utilization, an increase in ATPase activity, a disruption of the photosynthetic system, and an increase in the production and release of microcystins (MCs). However, these effects are highly dependent on the growth stage of the cyanobacterial cell and the magnitude of the added P concentration. In addition, exposure to a high concentration (10 μM) of BPA significantly stimulated the production of 20.7% more and the release of 29.2% more MCs from M. aeruginosa cells at a low P level. The responses of reactive oxygen species (ROS), superoxide dismutase (SOD) and malondialdehyde (MDA) suggested that exposure to BPA exposure at a low P level can lead to oxidative stress in M. aeruginosa. In addition, the differentially expressed 63 metabolites showed that cell growth, energy generation and photosynthesis were mainly regulated by the metabolic network of 3-phosphoglyceric acid (3-PGA), D-glucose 6-phosphate, UDP-α-D-galactose and UDP-N-acetyl-D-galactosamine (UDP-GalNAc) metabolism. Amino acids and lipid metabolism collectively mediated MCs production and release. These findings will provide important references for the control of harmful cyanobacterial blooms under combined pollution.