To reveal the implications of iron deficiency in the occurrence of harmful algal blooms, the physiological status of Prorocentrum micans Ehrenberg (Dinophyceae) was observed through laboratory-culture experiments at different iron levels. The results showed that iron deficiency led to a slowdown in growth rate of algal cells, a twisted structure, and metamorphosed function of chloroplast and mitochondrion. When iron supply was sufficient to meet the algal requirement, it could promote their development and metabolism and facilitate the uptake of micronutrients. Cellular Fe increased with increasing Fe level in the range of 0–10 µM. Low irradiance resulted in an increased uptake of Fe as well as Zn, Mn, and Co. The cellular molar ratio of P : Fe was ∼356 : 1, implying a synergistic uptake of phosphorus and iron. These findings are important in understanding crucial limiting factors during harmful algal blooms in natural environments.