A semiconductor device and method of manufacturing the same is provided in the present invention. The method includes the step of forming first mask patterns on a substrate, wherein the first mask patterns extend in a second direction and are spaced apart in a first direction to expose a portion of first insulating layer, removing the exposed first insulating layer to form multiple recesses in the first insulating layer, performing a surface treatment to the recess surface, filling up the recesses with a second insulating layer and exposing a portion of the first insulating layer, removing the exposed first insulating layer to form a mesh-type isolation structure, and forming storage node contact plugs in the openings of mesh-type isolation structure.