The invention discloses a manufacturing method of a super junction device. The method comprises the following steps: the step 1, forming a gate structure which is a trench gate, filling a gate trenchwith a polysilicon gate in the forming process of the trench gate, then carrying out first planarization to enable the surface of a first epitaxial layer with the trench gate to be a flat surface, andenabling the width of the gate trench at the leading-out position of the gate structure to meet the requirement of forming a contact hole; and the step 2, forming a super junction in the first epitaxial layer with the flat surface on which the trench gate is formed, wherein in the forming process of the super junction, a second epitaxial layer is adopted to fill the super junction trench, and then secondary planarization is performed, so that the surface of the first epitaxial layer with the super junction is a flat surface. According to the invention, the full-flat process can be realized, the trench gate process can be conveniently arranged before the super junction forming process, and the thermal process after the super junction is formed can be reduced, so that the mutual diffusion of impurities of the super junction is reduced, the device performance is improved, a photomask can be saved, and the process cost is reduced.