The present invention discloses a semiconductor overlapped PN structure and manufacturing method thereof. The method includes: providing a substrate; providing a first mask to define a P (or N) type well and at least one overlapped region in the substrate; implanting P (or N) type impurities into the P (or N) type well and the at least one overlapped region; providing a second mask having at least one opening to define an N (or P) type well in the substrate, and to define at least one dual-implanted region in the at least one overlapped region; implanting N (or P) type impurities into the N (or P) type well and the at least one dual-implanted region such that the at least one dual-implanted region has P type and N type impurities.