A manufacturing method of a semiconductor structure having an array area and a periphery area is provided. The manufacturing method includes the following steps. A substrate is provided. A plurality of trenches is formed on the substrate. The plurality of trenches is filled with insulating material to form at least one first insulating layer. A polysilicon layer is deposited on the substrate and the first insulating layer. A photoresist mask is formed on the periphery area. A portion of the polysilicon layer on the array area is etched, such that a top surface of the polysilicon layer on the array area is higher than the first insulating layer and lower than a top surface of the polysilicon layer on the periphery area. The photoresist mask is removed. A planarization process is implemented to remove a portion of the polysilicon layer on the array area and on the periphery area.