The invention discloses a polypeptide magnetic nanoparticle. The polypeptide magnetic nanoparticle comprises a specific targeting polypeptide and a magnetic nanoparticle, wherein the amino acid sequence of the specific targeting polypeptide is VRRDAPRFSMQGLDA-X, and the number of the C tail ends X of the specific targeting polypeptide is 5-20, preferably 5-15, and more preferably 9-12; preferably,amino acids in the X amino acid sequence are selected from one or more of C, G and N. The polypeptide nano magnetic bead technology can be used for CTC detection and molecular typing of various cancer types, including esophageal cancer, liver cancer, lung cancer, stomach cancer, breast cancer, colorectal cancer, cervical cancer and the like. The CTC molecular typing biomarker is prepared from PD-L1, HER2, ER, PR, AR, EGFR, CXCR4 and the like. The kit is beneficial to CTC detection and qualitative and semi-quantitative analysis of the expression level of the biomarker at the CTC level, so thattargeted individual targeted therapy or immunotherapy and other precise therapy are carried out on patients.