Disclosed is a method of manufacturing high quality lube base oil (Group III) from unconverted oil having various properties obtained in a variety of hydrocrackers using improved catalytic dewaxing and hydrofinishing, the method including producing unconverted oil of at least one kind in the same or different hydrocrackers; subjecting the unconverted oil to vacuum distillation; supplying all or part of the distillate fractions to a catalytic dewaxing reactor; supplying the dewaxed oil fraction to a hydrofinishing reactor; and stripping the hydrofinished light oil fraction, wherein make-up hydrogen is supplied upstream of the hydrofinishing reactor to increase hydrogen partial pressure, thereby enabling high quality base oil to be manufactured at high yield under optimal process conditions using unconverted oil produced by hydrocracking under various conditions.