The present invention discloses a super junction groove filling method. The method comprises the following steps: the step 1, providing a semiconductor wafer having a surface with a first conduction type epitaxial layer; the step 2, forming a hard mask layer, and performing lithography and etching to form a plurality of grooves; the step 3, performing first epitaxial growth to form a first layer second conduction type epitaxial layer to fill the grooves and stopping after the epitaxial layers in the grooves in the edge regions are completed combined, and forming a V-shaped opening at the middle area of the tops of the grooves at the central region after stopping; the step 4, taking the hard mask layer as a termination layer to perform etchback of the first layer second conduction type epitaxial layer; and the step 5, performing second epitaxial growth to form a second layer second conduction type epitaxial layer to completely fill the V-shaped openings of the grooves of the central area. The super junction groove filling method can improve in-plane uniformity, reduce the defect generation join improve the device performance.