The invention relates to a hepatitis B virus multi-epitope fusion protein and a preparation method and application thereof. The fusion protein is obtained by inserting hepatitis B virus multi-epitope fusion peptide (with the sequence shown as SEQIDNo.1) formed by serially connecting HBsAg313-321, HBsAg335-343, Pol150-159, Pol455-463 and Padre epitopes through connecting peptide between amino acid at the 78th position and amino acid at the 79th position of a hepatitis B virus core protein; and the preparation method comprises the following steps of: constructing a hepatitis B virus multi-epitope fusion protein expression plasmid pET28-HBc-HP; performing isopropyl thiogalactoside (IPTG) inducing expression by using an Escherichia coli expression system; and purifying by using affinity chromatography. The fusion protein carries a plurality of supertype epitopes of hepatitis B surface antigen (HBsAg), hepatitis B core antigen (HBcAg) and polymerase, is viral particles, has the advantages of strong immunogenicity, wide applicable range and the like, and can be used for preparing therapeutic hepatitis B vaccines.