The invention provides a porcine circovirus type 3 (PCV3) genetic engineering subunit vaccine and a preparation method thereof. The method comprises the following steps: S1, constructing a PCV3cap protein gene cloning vector; S2, carrying out splicing and expression screening on a PCV3cap protein gene cloned by S1, and determining a splicing manner; S3, optimizing a codon for expressing the PCV3cap protein gene screened by S2; S4, fusing and connecting a specific gene segment with the upstream of a PCV3cap protein gene N-end gene optimized by S3; S5, constructing expression engineering bacteria by utilizing the gene recombined by S4, and expressing soluble PCV3cap protein by adopting the expression engineering bacteria, wherein the subunit molecular weight is about 25 kDa; purifying the soluble PCV3cap protein; S6, obtaining purified protein which is circovirus sample particles with the diameter of 17.74 nm to 18.20 nm under an electron microscope, and adding an immunoenhancer into thepurified expression protein to prepare the vaccine. After experiment pigs are immunized by utilizing the vaccine, an antibody, which resists the PCV3cap protein, can be detected, and the PCV3 virus loading amount in blood serum of the experiment pigs can be remarkably reduced in a anti-virus protection experiment; the vaccine has a remarkable protection effect on the experiment pigs.