The present invention discloses a high voltage device and a manufacturing method thereof. The high voltage device is formed in a first conductive type substrate, wherein the substrate has an upper surface. The high voltage device includes: a second conductive type buried layer, which is formed in the substrate; a first conductive type well, which is formed between the upper surface and the buried layer; and a second conductive type well, which is connected to the first conductive type well and located at different horizontal positions. The second conductive type well includes a well lower surface, which has a first part and a second part, wherein the first part is directly above the buried layer and electrically coupled to the buried layer; and the second part is not located above the buried layer and forms a PN junction with the substrate.