The present invention provides gold nanocluster-liposome composite nanoparticles, which are a gold nanocluster encapsulated with a liposome vesicle, wherein the surface of the liposome vesicle is modified with distearoyl phosphatidylethanolamine-polyethylene glycol, the surface of the gold particle in the gold nanocluster is modified with a penetrating peptide and is bound to Cas9 protein and guiding ribonucleic acid, and the liposome vesicle comprises dioleoyl phosphoethanolamine, 2,3-dioleyloxypropyltrimethyl ammonium chloride and cholesterol. The invention further provides a preparation method and applications of the gold nanocluster-liposome composite nanoparticles. According to the present invention, by using the gold nanocluster-liposome composite nanoparticles, the CRISPR/Cas9 system can be efficiently delivered into cells without any other transfection reagents so as to improve the cell intake rate and the transfection efficiency, such that the gene treatment effects on a variety of tumors can be achieved, and the tracing effect can be achieved.