The present invention provides a method for manufacturing a deep-trench super PN junction. The method includes: a deposition step for forming an epitaxial layer on a substrate; forming a first dielectric layer and a second dielectric layer in sequence on the epitaxial layer; forming deep trenches in the epitaxial layer; completely filling the deep trenches with an epitaxial material and the epitaxial material is beyond the second dielectric layer; filling the entire surface of the second dielectric layer and the epitaxial layer such as Si using a third dielectric to from a surface filling layer with a predetermined height; etching back on the surface filling layer to the interface of the first dielectric layer and the epitaxial layer; and a removing step for removing the first dielectric layer, the second dielectric layer and the surface filling layer to planarize Si epitaxial material.