In order to investigate the toxic effects and energy distribution of photosynthetic system in algae exposed to heavy metal cadmium, the growth, chlorophyll-a, chlorophyll fluorescence and the energy model of PSII were measured in Cylindrospermopsis raciborskii cultured at different cadmium concentrations. The results showed that it had no significant effect on the chlorophyll-a content per cell and PSII photochemical activity of C. raciborskii after 96 h exposed to 0.2 mg/L Cd²⁺, while chlorophyll-a content per cell only 62.97% of the control group was found after 96 h exposed to upon 0.5 mg/L Cd²⁺. A significant inhibition in the photosynthesis of C. raciborskii when cultured in the media containing upon 5 mg/L Cd²⁺, and as quantum yield distribution parameters, φEo and ψo also showed a reduction by 15.35% and 13.52%. Moreover, the energy distribution of PSII, such as TR_O/CS_m and ET_O/CS_m, was significantly decreased and DI_O/CS_m did not markedly vary in algae cells. However, ABS/RC, TR_O/RC and DI_O/RC markedly increased in thylakoid, which significantly distinguished from treatments of 0.2, 0.5 and 1 mg/L Cd²⁺. These results suggested that the PSII reaction center was an important action site on the photosynthesis of C. raciborskii and the electron transfer on the donor side was inhibited when exposed to high cadmium concentration of more than 5 mg/L. However, the damage of photosynthetic structure might be protected and alleviated in C. raciborskii through the change of PSII energy distribution.