The present invention relates to a high voltage transformer with high magnetic leakage and dual high voltage output, comprising a base and a core set, wherein the base contains a hollow support into which a first core of the core set pierces, and primary coils are wound on both sides of the hollow support, while a plurality of isolation channels is installed for winding first and second secondary coils on external sides of primary coils. First and second slots are opened between the primary coils and the first and second secondary coils respectively, and both slots cut into an internal through hole. When a second core of the core set is placed at one end of the hollow support, extensions at both ends of the second core go through both sides of the first core, together with first and second protrusive parts between the two extensions that are installed within the first and second slots and combined with the first core to form multiple magnetic paths.