A transdermal drug delivery system was prepared by high methoxyl pectin (HMP) or low methoxyl pectin (LMP) coated vitamin C liposomes. HMP coated vitamin C liposomes (HMP-L) and LMP coated vitamin C liposomes (LMP-L) exhibited an increase in average diameter (from 66.9 nm to 117.3 nm and 129.6 nm, respectively), a decrease in zeta potential (from −2.3 mV to −23.9 mV and −35.5 mV, respectively), and a similar entrapment efficiency (48.3–50.1%). Morphology and FTIR analysis confirmed that pectin was successfully coated on the surface of vitamin C liposomes mainly through the hydrogen bonding interactions. Besides, HMP-L and LMP-L exhibited an obvious improvement in storage stability, with lower aggregation, oxidation of lipid and leakage ratio of vitamin C from liposomes, and LMP-L showed better physicochemical stability than HMP-L. Moreover, skin permeation of vitamin C was improved 1.7-fold for HMP-L and 2.1-fold for LMP-L after 24 h, respectively, compared with vitamin C nanoliposomes. Therefore, this study suggested that pectin coated liposomes, especially the LMP-L, could be a promising transdermal drug delivery system with better storage stability and skin permeation.