The present invention discloses a high voltage device and a manufacturing method thereof. The high voltage device includes: a first conductive type substrate in which isolation regions are formed for defining a device region; a gate formed on the first conductive type substrate; a source and a drain formed in the device region and located at both sides of the gate respectively, and doped with second conductive type impurities; a second conductive type well, which is formed in the first conductive type substrate, and surrounds the drain from top view; and a first deep trench isolation structure, which is formed in the first conductive type substrate, and is located in the second conductive type well between the source and the drain from top view, wherein the depth of the first deep trench isolation structure is deeper than the second conductive type well from the cross-sectional view.