The invention relates to a duck short beak dwarf syndrome gene engineering subunit inactivated vaccine and a preparation method thereof. Aiming at a variant strain, the VP2 gene of the SBDS-GPV JS01 strain is subjected to codon optimization and is cloned to a baculovirus vector, so that a recombinant baculovirus rBac-JS01VP2 strain is successfully constructed; insect cell full suspension (or spinner bottle) culture is adopted, the technology is mature, and production transformation and step-by-step amplification culture are facilitated; compared with traditional duck embryo or duck embryo fibroblast culture, the virus titer is high, the quality is stable, the production period is short, and the cost is low; compared with an antibody product, the protection rate is high, the duration time of a maternal antibody is long, only female ducks are immunized, and labor and cost are saved; serum or egg source miscellaneous protein does not exist, and the side reaction is extremely low; the expressed VP2 protein can be assembled into virus-like particles (VLPs), and the immunogenicity is good; the expression quantity is high (when the virus titer is 8.0 Log10TCID50/ml, the VP2 protein expression quantity reaches 50-100 mg/L), the antibody level is high, and the lasting time is long; the shelf life of the product is 18 months, and the immune period is 6 months; and the ELISA antibody detection method is used for screening susceptible ducks and evaluating efficacy.