The invention provides a super-junction silicon carbide device and a preparation method thereof. The preparation method includes growing a first epitaxial layer with a first conductive type on the right side of a silicon carbide substrate with the first conductive type; forming one or more trenches in the first epitaxial layer; and successively growing a plurality of second epitaxial layers with a second conductive type in the trenches from the bottom to the top until the filling of the trenches is completed, and forming a super-junction structure. Compared with the prior art, the super-junction silicon carbide device and the preparation method thereof provided allow the plurality of second epitaxial layers with the second conductive type in the trenches from the bottom to the top until the filling of the trenches is completed to form the super-junction structure, the number of the epitaxial layers and the thickness of each epitaxial layer can be adjusted according to the depth of the trenches, the gapless filling of the trenches can be realized, the problem that the top of the trenches is sealed in advance can be prevented, and meanwhile, the preparation method is simple in process, low in cost, and is convenient for industrialized production of the super-junction silicon carbide.