This invention presents a method for preparing casein-based silica dual drug-loaded composite microcapsule. Recently, casein has shown good application prospects in the field of medicine due to its good biocompatibility and unique cavity structure. However, research on preparation of casein-based dual drug-loaded microcapsules is still rarely reported. In this invention, dual drug-loaded casein microcapsules is obtained via interfacial polymerization method, where drug-loaded casein can be used as outer shell material in capsule, and silica is served as inner shell in the capsule. In the obtained microcapsule, drugs can not only be loaded in the inner cavity, but also in casein shell. Application of the dual drug-loaded microcapsules in the treatment of diseases is expected to reduce the number of dose to a certain extent and improve the therapeutic effect.