Blooms of harmful cyanobacteria have been observed in various water bodies across the world and some of them can produce intracellular toxins, such as microcystins (MCs), which negatively impact aquatic organisms and human health. Iron participates significantly in cyanobacterial photosynthesis and is proposed to be linked to MC production. Here, the cyanobacteria Microcystis aeruginosa was cultivated under different iron regimes to investigate the relationship between photosynthetic capacity and MC production. The results showed that iron addition increased cell density, cellular protein concentration and the Chl-a (chlorophyll-a) content. Similarly, it can also up–regulate photosynthetic capacity and promote MC–leucine–arginine (MC–LR) production, but not in a dose–dependent manner. Moreover, a significant positive correlation between photosynthetic capacity and MC production was observed, and electron transport parameters were the most important parameters contributing to the variation of intracellular MC–LR concentration revealed by Generalized Additive Model analysis. As the electron transport chain was affected by iron variation, adenosine triphosphate production was inhibited, leading to the alteration of MC synthetase gene expression. Therefore, it is demonstrated that MC production greatly relies on redox status and energy metabolism of photosynthesis in M. aeruginosa. In consequence, more attention should be paid to the involvement of photosynthesis in the regulation of MC production by iron variation in the future.