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This invention provides a transdermal follicular delivery system for active ingredients based on a protein carrier. The system comprises a composite structure of a small molecule active ingredient, a bioactive protein, and a polymer shell, with a size of 40-150 nm and a polymer shell thickness of 10-70 nm. The zeta potential of this protein carrier-based transdermal follicular delivery system is positively charged. The small molecule active ingredient is loaded within the bioactive protein, and the polymer shell coats the bioactive protein to form a protein nanogel. Both the small molecule active ingredient and the bioactive protein have beneficial effects on hair follicles. When this transdermal follicular delivery system is applied to the surface of a hair follicle or skin, the functional small molecules are delivered transdermally along with the nanogel to the interior of the hair follicle and surrounding tissues, where they are released in a controlled manner, thus effectively exerting their effects.