Abstract: Mercury (Hg) pollution is a global environmental problem and a major hazard to human health. Investigating the interactions between algae and Hg can provide a scientific basis for the assessment of Hg toxicity and ecological risk in aquatic ecosystems, as well as the bioremediation of Hg pollution. In this study, we selected Chlamydomonas nivalis as the object due to its strong adaptive ability to Hg, aiming to understand how algal cells respond to mercury stress and its tolerance mechanism. The results showed a time-dependent quantitative relationship between Hg²⁺ stress and algal cells, with a 48h half-effect concentration of 1.44 mg/L. Compared with the control group, algal cells subjected to low concentrations of Hg²⁺(≤1.5 mg/L) maintained growth and photosynthetic activity. The biomass and pigment content of the 2.0 mg/L Hg²⁺ treated group did not change significantly (P>0.05) at 6h of stress, but both decreased significantly (P<0.05) at 48h. As Hg²⁺ concentration and exposure time increased, the maximal photochemical efficiency, the maximum electron transfer reaction, half-saturation light intensity, and light use efficiency were reduced. Algal cells experienced inhibited photosynthetic electron transfer, as evidenced by notable alterations in rapid fluorescence-induced kinetic curve and \rmQ^-_\rmA reoxidation. Hg²⁺ stress disrupted energy flow, inactivated reaction centers in algal cells, led to a significant increase in energy dissipation, and elevated the photosynthetic efficiency of active reaction centers, maintaining energy balance and metabolic activity. The damage to the photosynthetic system led to an increase in the cellular reactive oxygen species content, a decrease in the total soluble protein content, a significant increase in superoxide dismutase activity and a decrease in the reduced glutathione content. In this study, we confirmed that Hg²⁺ tolerance was strong in Chlamydomonas nivalis, and photosystem Ⅱ was the target of Hg²⁺; the photosynthetic energy allocation strategy and antioxidant system were the important detoxification mechanisms of cells against Hg²⁺ stress.