A method for preparing fluorescent-encoded microspheres coated with metal nanoshells is disclosed herein. By using SPG method, metal nano-material modified with a certain ligand is used as a new surfactant in the emulsification process, and different kinds and different amounts of fluorescent materials are doped into polymer microspheres to prepare fluorescent-encoded microspheres with different fluorescent-encoded signals and uniformly coated metal nanoshells in one step. The prepared fluorescent-encoded microsphere comprises a metal nanoshell, a polymer, and a fluorescent-encoded material. The fluorescent-encoded microsphere has a particle size of 1 μm˜20 μm, CV of less than 10%, which can be used for protein/nucleic acid detection. The preparation method has the advantages of simple process, high surface coating rate, good uniformity and controllable LSPR peaks, which can solve the problems of existing commonly used metal nanoshell coating methods such as low surface coating rate, poor uniformity, complex preparation process and uncontrollable local surface plasmon resonance (LSPR) peaks, etc.