The invention relates to a silicon carbide micro-channel heat dissipation structure of a three-dimensional integrated circuit and a manufacturing method thereof, and mainly solves the problem that a micro-channel wall material is low in heat conductivity and small in contact area with the micro-channel wall in the prior art. The silicon carbide micro-channel heat dissipation structure comprises an upper chip (1) and a lower chip (2), wherein each chip comprises a circuit layer (3), a silicon substrate (4), a silicon channel wall (5), a silicon carbide channel wall (6), a micro-channel (7) and a silicon micro-channel cap (8) from top to bottom, wherein each circuit layer is positioned on the top of the front side of the corresponding chip, and each silicon substrate is adjacent to the corresponding circuit layer and is positioned below the corresponding circuit layer; each silicon channel wall is adjacent to the corresponding silicon substrate and is positioned below the corresponding silicon substrate; each silicon carbide channel wall epitaxially grows below the corresponding silicon channel wall; the cross section of each micro-channel is of an integral structure with a semi-elliptical upper part and a rectangular lower part, and each micro-channel is positioned below the corresponding silicon channel wall. The heat dissipation contact area close to the circuit layers is increased, the distances with the circuit layers are shortened, and the heat dissipation performance of the micro-channel heat dissipation structure is improved.