The invention discloses a clean fuel production method. According to the clean fuel production method, raw oil enters an atmospheric tower, fuel oil is fractionated from a side line of the atmospheric tower and is mixed with hydrogen, the mixture of the fuel oil and hydrogen enters a hydrogenation reactor, efflux of the hydrogenation reactor enters a stripping tower to be in contact with a stripping medium, and a stripped product enters a product tank. According to the clean fuel production method, the consumption of resources and energy sources is reduced, and the investment cost and the operation cost are lowered.