Chalcone synthase (CHS), a key enzyme in plant flavonoid synthesis, is essential for plant tolerance to abiotic stress. However, little research on CHS from the earliest terrestrial plants, such as mosses, has been reported. Here, the biological function of a CHS gene from Antarctic moss Pohlia nutans (PnCHS1) was studied. PnCHS1 had a 32.8–53.7% similarity to CHS from other species, however it still had highly conserved motifs of CHS such as Catalytic site (Asn366, His333) and Co-A binding site (Ser146). Subcellular localization analysis showed that PnCHS1 was distributed in the cell membrane and in the membranes of endothelial organelles. Heterologous expression of PnCHS1 increased flavonoid content in 5-day-old Arabidopsis grown with 24 h light and 17-day-old Arabidopsis cultured with sucrose, as well as anthocyanin content in the latter. PnCHS1 heterologous expression in Arabidopsis increased plant tolerance to salt stress, including a high germina- tion rate and a long taproot. Heterologous expression of PnCHS1 boosted tolerance to oxidative stress while decreasing the sensitivity to ABA. Under H2O2 or ABA stress, the expression pattern of PnCHS1, ROS scavenging enzyme gene (FeSOD1, FeSOD2, Cu-Zn-SOD2, and Cu-Zn-SOD3) and three genes of ABA signal pathway (RAB18, RD29B, and NCED3) were considerably up-regulated by real-time quantitative analysis. It indicates that PnCHS1 could enhance plant tolerance to NaCl and oxidative stresses, and may play a role in the adaptation of Antarctic moss to extreme environments.