The invention relates to a preparation method of a phycoerythrin ratio fluorescence sensor based on a magnetic molecular imprinted nucleus/shell polymer. A Fe3O4 magnetic nano-particleis used as the center, the surface of the Fe3O4 magnetic nano-particleis coupled with blue fluorescence emitting carbon quantum dots B-CDs, a SiO2 shell layer loaded with template molecule phycoerythrin generates onthe surfaces of the Fe3O4/B-CDs, and template molecule elution is conducted to prepare magnetic molecular imprinted nucleus/shell polymer Fe3O4/B-CDs/SiO2-MIPs. The polymer dispersion liquid fluorescence emission spectra under different phycoerythrin concentration are measured, the linear relation between the fluorescence emission peak intensity ratio I/I of the phycoerythrinto the B-CDs and the phycoerythrin molar concentration is fitted, and a phycoerythrin ratio fluorescence sensor is constructed. Compared with the prior art, the method is simple to operate and low incost, raw materials are easy to obtain, ratio signal interference resisting capacity is high, accuracy is high, flexibility and selectivity are high, and a novel ratio fluorescence sensor can be developed and used for efficient phycoerythrin detection.