Perfluorooctanesulfonic acid (PFOS) is widely detected in the aquatic environment. More attentions were paid to its acute biotoxicity at high-dose concentrations, whereas the actual long-term effect (hormesis or inhibition of growth) of PFOS with environmental concentrations on marine phytoplankton remains unclear. In this study, marine Chlorella sp. was exposed to PFOS at low concentrations (100 ng/L, 10 μg/L, and 1 mg/L) for 26 days. The hormesis effect disappeared at the population level on Day 18, but persisted at the molecular and cellular levels on Day 24, suggesting that the stimulatory hormetic effect induced by low-level PFOS (approximating environmental concentrations) does not persist throughout algal life cycle at population level. The 100 ng/L and 1 mg/L PFOS treatments caused algal cell to swell and shrink, respectively. The low-level PFOS treatments could accelerate cells apoptosis and induce cell necrosis at 100 ng/L. Specifically, the energy metabolism associated with carbohydrate metabolism and amino acid metabolism was significantly up-regulated as well as the reduced chlorophyll content (related to the down-regulation of porphyrin metabolism) to combat the 100 ng/L PFOS rather than be engaged in divide and growth. Additionally, the decreased biomass in the 100 ng/L treatment was also attributed to certain proteins associated with down-regulations of carotenoid biosynthesis, thiamine metabolism, non-homologous end-joining, and nitrogen metabolism along with the increased oxidative stress. Our findings provide a new insight into the long-term ecological effect of PFOS at environmental concentrations.