The present invention relates to a method of preparing a microcapsule with a double-layered structure which comprises the steps of performing an interfacial polymerization of an amine-aldehyde prepolymer on droplets containing an inorganic metal precursor selected from carboxylate and alkoxide compounds, and hydrolyzing the including inorganic precursors for formation of inorganic inner layer. The method of the present invention can prepare a microcapsule with a double-layered structure of an inorganic inner layer and a polymer outer layer, which is effective for eluting and substituting a core material inside the capsule.