A novel molecularly imprinted polymers (MIPs) coated micro-stir bar (MSB) for Glibenclamide (GM) was developed. The MIPs, with GM as template molecular and methacrylic acid as functional monomer, were synthesized at the surface of the silylated MSB that was filled with magnetic core as substrate. Computational simulation was used for the optimal selection of functional monomers and porogen. The thickness of MIPs coating for MSB was about 10 μm, the adsorption and desorption time were about 40 and 20 min, respectively. The MIPs coated MSB possessed mechanical stability, high adsorption capacity, and good selectivity for GM. To achieve the optimum extraction performance, several parameters including extraction and desorption time, stirring rate, extraction and desorption solvent were investigated. A method for the determination of GM in herbal dietary supplements by MIPs coated MSB coupled with HPLC-UV was established. The results exhibited good linear ranges of 10–6250 μg L−1 with the low limit of detection of GM (3.05 μg L−1) and the good recoveries (81.9–101.4%).