Mercuric chloride (HgCl2) is a common heavy-metal pollutant widely used in commercial products and industry, but its excessive use and uncontrolled discharge have caused great harm to aquatic environments and human health. To research the mechanisms of HgCl2 toxicity in aquatic organisms, this study cultured the green alga Scenedesmus quadricauda in a gradient of HgCl2 concentrations (0, 0.1, 0.3, 0.5, 0.7, and 0.9 mg/L) for 9 days. The results showed that: (1) when the concentrations of HgCl2 were high (≥0.7 mg/L), the toxic effects completely inhibited the growth of algal cells, the culture liquid changed from green to light yellow, and cells aggregated and sank to the bottom. Submicroscopic structural imaging showed that at 0.9 mg/L HgCl2, the algal cells were seriously damaged and obvious plasma–wall separation occurred. Furthermore, the arrangement of photosynthetic lamellae became disordered and the nuclei and protein nuclei faded or even disappeared. (2) When the concentrations of HgCl2 were low and medium (≤0.5 mg/L), the activity of superoxide dismutase (SOD) in algal cells increased in the first five days, but the degree of increase was smaller than in the control group. However, under high HgCl2 concentrations (≥0.7 mg/L), the activity of SOD began to decrease sharply on the seventh day. The activity of peroxidase (POD) decreased more obviously than that of SOD. (3) Under medium and high HgCl2 concentrations (≥0.5 mg/L), the content of malondialdehyde (MDA) in algal cells increased over time, and had not decreased again by the last day of measurement. In contrast, the contents of total protein (TP) and soluble sugar (SS) both exhibited decreasing trends under high HgCl2 concentrations. (4) When the HgCl2 concentrations were ≥0.7 mg/L, the content of photosynthetic pigments in algal cells decreased, and the light quantum yield of PS Ⅱ decreased. At the same time, as culture time progressed, the photosynthetic electron transfer and energy-conversion efficiency were seriously damaged and photosynthesis never returned to normal levels. This research provides a reference for understanding the mechanism by which HgCl2 pollution affects aquatic ecosystems and may help with pollution management in the future.