An isolation structure for an N epitaxy-based silicon carbide device, comprising an N-type substrate, wherein an N-type drift region is arranged on the N-type substrate, a first isolation trench in which an oxide is deposited and a second isolation trench in which the oxide is deposited are arranged on the N-type drift region to form a high-voltage region, a low-voltage region and a level shift region, a second P-type doped region is arranged at a bottom of the low-voltage region and a bottom of the level shift region, a second N-type doped region is arranged on the second P-type doped region in the low-voltage region, and back-to-back PN junctions are formed by the N-type drift region, the second P-type doped region in the low-voltage region and the second N-type doped region.