A fuse structure and a manufacturing method thereof are provided. The fuse structure includes: a substrate; an active region positioned above the substrate; a fuse gate structure surrounding a circumferential outer surface of the active region and electrically connected to a first power source; and a control gate structure surrounding a circumferential outer surface of the fuse gate structure and electrically connected to a second power source. A voltage of the first power source is greater than that of the second power source.