Rutin, a flavonoid glycoside phytochemical compound, has a remarkable antiobesity effect. However, its therapeutic potential is hindered by its poor water solubility and low oral bioavailability. In this study, rutin was loaded into liposomes (LR) through the self-assembly of lecithin and cholesterol. It was discovered that liposomes improved the water solubility and cellular uptake of rutin in adipocytes. These rutin-loaded liposomes were then incorporated into a microneedle patch (MP) system formed by polyvinylpyrrolidone and poly(vinyl alcohol), and the MP-LR showed an increased release percentage in the adipose tissue microenvironment of pH 6.5 and achieved local delivery of rutin into adipocytes. Next, the therapeutic potentials of rutin, LR, and MP-LR were investigated in a high-fat diet (HFD)-induced obese mouse model. The MP-LR formulation decreased the weight of the HFD mice the most significantly. The antilipogenesis mechanisms of MP-LR are downregulating the lipid synthesis-related proteins (PPAR γ and C/EBP α) in adipocytes and promoting the expression of the beige adipogenesis-related proteins (UCP 1 and Cyt C). The MP systems further promote the local penetration of LR into the adipose tissue specifically, which again elevates their antiobesity effect. Overall, this study suggests that MP-delivered liposome-based formulation is a promising approach to enhance the antiobesity efficacy of antilipogenesis bioactive compounds.