The invention discloses an acne-removing, mark-eliminating and skin-protecting multifunctional preparation with both acne-removing and mark-eliminating effects and skin-beautifying and skin-protecting effects and a preparation method thereof. The acne-removing, mark-eliminating and skin-protecting multifunctional preparation is composed of a skin care composition, an acne-removing and mark-eliminating composition and a solvent, and not only contains collagen, vitamins and other various nutrients required for normal skin nutrition, but also contains a coenzyme I, a coenzyme II, nicotinamide, a coenzyme Q10 and other healthcare components required for skin health maintenance. The acne-removing, mark-eliminating and skin-protecting multifunctional preparation not only has disinfection, anticorrosion and anti-bacterium components, but also has injured tissue repair components, and the effective combination of the multiple components can generate mild acne-removing and mark-eliminating effects; the acne-removing, mark-eliminating and skin-protecting multifunctional preparation has the advantages of being high in safety, convenient to use, wide in application range, excellent in effect and the like. The acne-removing, mark-eliminating and skin-protecting multifunctional preparation disclosed by the invention is non-toxic, free from irritation and allergy and almost suitable for all people. The preparation method of the acne-removing, mark-eliminating and skin-protecting multifunctional preparation, disclosed by the invention, has the advantages of mild condition, no need of temperature rise, low energy consumption, simple and short process flow and no environmental pollution, and is a green manufacturing technology that is worth of being popularized.