Nanostructured lipid carrier (NLC) is a new colloidal delivery system which can effectively solve the problems of stability and transdermal delivery of active ingredients with poor water solubility and biocompatibility. Coenzyme Q10 (CoQ10), as a lipophilic antioxidant, has poor chemical stability due to unsaturated double bonds in its molecular structure, which limits its addition and application in cosmetics. In this study, CoQ10 NLC was prepared using the mixture of Caprylyl/Capryl Glycoside (APG) and quaternized chitosan (QCS). The particle size of the QCS–APG–NLC was around 250 nm. Compared to NLC stabilized by APG, QCS–APG–NLC has better storage stability under high temperature and light conditions. In vitro transdermal experiment analysis and confocal laser scanning microscopy (CLSM) observation found that QCS modification can effectively increase the penetration amount of CoQ10 in the skin. So, it is suggested that QCS modified APG–NLC can be used as an effective transdermal delivery system for lipophilic active components.