Heterocapsa bohaiensis is a newly identified dinoflagellate species that causes harmful blooms in coastal areas in China, Malaysian, and New Caledonian. These blooms have led to substantial economic losses for local aquaculture. Previous studies have mainly focused on understanding the toxicity of H. bohaiensis. However, the causes of H. bohaiensis blooms remain unknown. In this study, we aimed to ascertain nitrogen (N) and phosphorus (P) requirements for the growth and reproduction of H. bohaiensis. Additionally, we sought to understand the functional mechanisms by comparing the transcriptomes of H. bohaiensis under nutrient-limited conditions and control conditions. The results revealed a wide range of acceptable N:P ratios for H. bohainensis, attributed to a mechanism involving nutrient storage, which allowed H. bohainensis to sustain its growth even when either nitrate or phosphate was depleted. Higher N:P ratios (> 27.5) were more conducive to the growth of H. bohainensis than f/2 medium or low ratios, which is related to the N:P ratios absorbed by H. bohainensis. The toxicity of H. bohainensis was significantly enhanced in N-limited or P-limited states. These findings underscore the significance of the physiological metabolism of H. bohainensis in adapting to environmental stresses induced by human activities and establishing the dominance of blooms.