The toxic Prorocentrum lima complex can potentially cause serious harm to the benthos and entire food chain. Studies have revealed physiological differences in strains from different regions related to local environment, while differences in the adaptive responses of P. lima complex should be urgently assessed. Hence, this study explored the adaptive responses to varying light intensities and photoperiods of two P. lima complex strains SHG101 and 3XS34, isolated from the Bohai Sea and the South China Sea, respectively. We found the highest cell density of 7.49 × 104 cells mL−1 recorded in the 3XS strain in the stationary phase with high light intensity exposure. No significant difference was observed in growth rate among SHG groups, however, significant differences were found among 3XS groups ranging from 0.176 to 0.311 d−1. Three key pigments Chl a, Peri, and Fuco accounted for up to 60% of the total pigments. Production and concentrations of pigments and Fv/Fm values exhibit a significant negative correlation with high light intensity and growth. Conversely, total diarrhetic shellfish toxin content and the proportion of diol esters increased to varying degrees after high intensity light exposure, with 3XS strain under high light intensity and a photoperiod of light and darkness (12L:12D) consistently exhibiting the highest levels, finally reaching a maximum (21.6 pg cell−1) at day 28. A shortened photoperiod of high light intensity (8L:16D) resulted in impaired recovery compared with 12L:12D. Furthermore, 3XS showed more delayed and intense adaptive responses, indicating a stronger tolerance compared to SHG. Collectively, these results directly characterized variation in the adaptive responses of geographically distinct strains of P. lima complex, highlighting the previously ignored potential risk diversity of this species.