Dinoflagellates are ubiquitous marine primary producers and the main organisms responsible for harmful algal blooms. Ocean warming and frequent marine heatwaves under climate change profoundly alter dinoflagellate physiology and community succession. The East China Sea, a typical Chinese marginal sea, has seen increasingly frequent summer heatwaves that significantly reshape phytoplankton communities. Dinoflagellates are classified into armored and unarmored forms based on thecal structure, a key trait leading to divergent thermal tolerance, repair capacity, and regulatory strategies. However, unified experimental comparisons of their temperature responses are scarce. Thus, examining their differential responses to warming and heatwaves is essential for predicting harmful algal bloom dynamics in the East China Sea under future warming. We examined armored and unarmored dinoflagellates across temperature gradients (17–29℃) using 12 species (6 armored, 6 unarmored), then selected two armored (Prorocentrum obtusidens, Prorocentrum minimum) and two unarmored (Karenia mikimotoi, Karlodinium veneficum) species for heatwave stress–recovery simulations based on physiological traits. The main results are as follows: (1) Armored dinoflagellates exhibited higher optimal growth temperatures (24.43-26.81℃), with particulate organic carbon and nitrogen generally maintained or increased under high temperatures. Unarmored species had lower optimal temperatures (23.10-24.88℃) and weaker thermal tolerance. (2) Armored dinoflagellates maintained growth under heat stress and rapidly recovered photosynthesis after temperature normalization. Unarmored species showed growth inhibition during stress or recovery, with delayed photosynthetic recovery. Transcriptomic analyses revealed that armored species maintained or upregulated genes involved in photosynthesis, carbon fixation, ROS scavenging, and membrane transport during stress, and enhanced protein repair and thecal remodeling during recovery. In contrast, unarmored species generally suppressed photosynthetic and antioxidant pathways during stress, initiating repair only during recovery. (3) The presence or absence of theca is the core driver of differential responses. Armored species maintained stable photosynthesis and metabolism while remodeling thecal components, buffering intracellular homeostasis and enhancing tolerance and recovery. Lacking this protection, unarmored species reduced metabolic investment under heat stress, leading to delayed recovery. Collectively, This study systematically compared armored and unarmored dinoflagellate responses to warming and heatwaves, revealing the core ecological role of thecal structure in thermal adaptation. The results offer novel functional-trait evidence for phytoplankton adaptation to extreme temperatures and a theoretical basis for predicting community succession and harmful algal bloom risks under global warming.

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