Four pairs of previously undescribed naturally occurring naphthoquinones G-J (1-4) along with seven known naphthoquinones (5-11), were isolated from the roots of Arnebia euchroma (Royle) Johnst, and compounds 9-11 naphthoquinones isolated from Boraginaceae for the first time. The structures of the new compounds were clarified by extensive analysis of spectroscopic data. Notably, naphthoquinones G-J were efficiently resolved by chiral HPLC to give four pairs of optically pure enantiomers. Pharmacological study revealed that all isolated compounds had obvious anti-proliferative activities toward HaCaT cells. The results of the anti-proliferation activity study in vitro showed that compounds 1 and 4 demonstrated the strongest inhibitory effects on HaCaT cells, the IC50 values ranged from 0 to 10 μM. Furthermore, the results from molecular docking studies exhibited that the more bioactive compounds 1 and 4 with significant anti-proliferative were found to have strong interactions with the EGFR enzyme.