The invention provides a preparation method of a core-shell type surface molecularly imprinted microsphere used for melamine detection. The preparation method comprises the following steps: firstly dispersing styrene and methacrylic acid monomers into water, and reacting under nitrogen atmosphere by taking potassium persulfate as an initiator, so that polystyrene microspheres rich in carboxyls on the surfaces are prepared; then carrying out reaction on melamine, methacrylic acid, phenylene bisacrylamide and azo-bis-iso-heptonitrile with the surfaces of the prepared polystyrene microspheres, so that melamine molecularly imprinted core-shell type microspheres are obtained, and eluting melamine imprinted molecules located in shell layers of the imprinted microspheres. Hole structures complementary in the structure, size and functional groups with the imprinted molecules are formed inside the shell layers, the core-shell type microspheres with the imprinted molecules eluted have functions of specifically identifying a target analyte melamine molecule and detecting sensitivity of the melamine molecule, and when spaces are close to each other, selective identification and detection on the target analyte melamine molecule are realized under the action of a concentration difference driving force.