Anthropogenic CO₂ emissions drive ocean acidification (OA). Trichodesmium, a key marine N₂ fixer, displayscontrasting growth responses to OA across morphotypes, with negative responses in free trichomes but neutral or positive in colonies. However, the lack of mechanistic understanding for these discrepancies has impaired our ability to predict the ecophysiological response of Trichodesmium in the changing ocean. Here, we developedecophysiological models of Trichodesmium and underpin mechanisms behind contrasting responses to OA by distinct morphological adaptations. For free trichomes, our diurnal model corroborated previous findings that OA impairs nitrogenase efficiency and photosynthetic energy production. In colonies, however, OA alleviated copper and ammonia toxicity within the microenvironment, potentially with increased iron acquisition synergies, outweighing the minor effects of inorganic carbon limitation relief in the colony center. Projections suggest that globally, OA will reduce N₂ fixation of trichomes by 16±6% but increase that of colonies by 19±24% within this century. By resolving morphotype-specific mechanisms, our study clarifies Trichodesmium’s adaptive strategies, which may enable it to sustain its competitiveness and biogeochemical impacts in the changing ocean.