Due to increasing anthropogenic perturbation and water eutrophication, cyanobacterial blooms (CYBs) have become a global ecological and environmental problem. Toxic CYBs and elevated pH are considered to be the two key stressors associated with eutrophication in natural waters, particularly in the event of CO2 depletion induced by dense blooms. However, previous research has been focused on investigating the impacts of toxic CYBs or pH changes in isolation, whereas the interactive effects of such stressors on edible bivalves that inhabit CYB waters still lack information. In this study, the combined effects of toxic Microcystis aeruginosa and pH shifts on the antioxidant responses, immune responses, and apoptosis of the edible freshwater bivalve Corbicula fluminea were explored. The results showed that the activity of antioxidant enzymes was significantly impacted by the interactive effects between toxic M. aeruginosa exposure and time course, yet pH shifts showed no significant effects on the activities of these antioxidant enzymes, implying that the antioxidant response in C. fluminea was mainly triggered by toxic M. aeruginosa exposure. Toxic M. aeruginosa also induced an increased production of reactive oxygen species and malondialdehyde in treated clams, particularly under high pH settings. The elevated lysosomal enzyme activity helped C. fluminea defend against toxic M. aeruginosa exposure under high pH conditions. The principal component analysis (PCA) and the integrated biomarker response (IBR) results suggested that the treated clams were subjected to the elevated toxicity of toxic M. aeruginosa in conditions of high pH. The heat shock proteins-related genes might be triggered to resist the oxidative damage in treated clams. Moreover, the upregulation of TNF and casp8 genes indicated the potential activation of the caspase8-mediated apoptotic pathway through TNF receptor interaction, potentially resulting in apoptosis. The TUNEL assay results further confirmed that apoptosis appeared in treated clams. These findings improve our understanding of the combined toxicological effects of harmful algae and pH shifts on bivalves, which will provide insights into a comprehensive ecological risk assessment of toxic CYBs to edible bivalve species.