The invention discloses a groove-type super junction which comprises a plurality of grooves. Each groove is filled with a first epitaxial layer of the second conductivity type. The smallest grooves in size tend to be full filled with the first epitaxial layer, the grooves which are not fully filled with the first epitaxial layer are also filled with a second epitaxial layer, the second epitaxial layer which is stacked on the surface of the first epitaxial layer fully fills each groove. The second epitaxial layer has no doping or doping of the second conductivity type with a lower doping concentration relative to the first epitaxial layer. The difference of doping between the second epitaxial layer and the first epitaxial layer makes the total doping amount of the thin layer of the second conductivity type determined by the first epitaxial layer. Thus, the impact on the breakdown voltage of the super junction by the size differences of the grooves is reduced, so that the uniformity in surface of the breakdown voltage of the super junction is improved. The invention further discloses a manufacturing method of the grooved super junction. The groove-type super junction and the manufacturing method thereof are capable of improving the uniformity in surface of the breakdown voltage of the super junction with a simple technology, which has an important significance in the quantity production of the platform of the super junction technology.