The ginger extract obtained with supercritical CO2 fluid was purified by molecular distillation (MD), and the chemical compositions, antioxidant and cytotoxic activities of ginger extract and its distillates were investigated. Analysis revealed that the ginger extract was rich in terpene hydrocarbons, along with oxygenated terpenes and other non‐volatile compounds. The MD distillates were prepared in a series of stages and the active compounds like terpenes and gingerols could be separated by MD. The major compounds of the distillates purified by MD at 40 °C, 80 Pa and 60 °C, 80 Pa were terpene hydrocarbons. Additional distillates obtained by MD at 80 °C, 80 Pa and 100 °C, 60 Pa were predominated by terpene hydrocarbons and oxygenated terpenes. Until the operating conditions of MD reached 150 °C and 2 Pa, some non‐volatile compounds were concentrated in the final distillate. Moreover, antioxidant activities and the cytotoxic effects on three human cancer cells in final MD distillate were superior to other extracts, and this phenomenon could be mainly supported by the phenols. The MD could be used to prepare ginger distillates with better antioxidant and cytotoxic activities.