The invention discloses a novel coronavirus subprotein nano vaccine and a preparation method and application thereof. The nano vaccine comprises: an organic compound self-assembled by polylactic acid, a porphyrin or a porphyrin derivative and a Co2+ ion conjugate; a novel coronavirus antigen protein; a vaccine adjuvant and lipid. According to the invention, a core of the synthesized organic compound is coated with the adjuvant, and the surface of the synthesized organic compound is efficiently loaded with the novel coronavirus antigen protein, so that a nano vaccine system for co-delivery of the novel coronavirus antigen protein and the vaccine adjuvant is implemented, and not only the immunogenicity of a novel coronavirus recombinant subprotein can be played to the greatest extent, but also the distribution condition of the nano vaccine in a living body can be traced through fluorescent molecules. In addition, the nano vaccine provided by the invention is also connected with polypeptide capable of specifically targeting antigen presenting cells, so that the nano vaccine is promoted to be massively ingested by DC cells, and the antiviral reaction is promoted. Meanwhile, the preparation method of the nano vaccine is simple and efficient, and a brand new way is provided for effective prevention of novel coronavirus infection.