A semiconductor memory device, a memory system including the same, a method of manufacturing the same and a method of operating the same are provided. The semiconductor memory device includes a pipe channel layer, vertical channel layers coupled to a top surface of the pipe channel layer, a first pipe gate substantially surrounding a bottom surface and side surfaces of the pipe channel layer, a boosting gate formed over the pipe channel layer, and first insulating layers and conductive layers alternately stacked over the boosting gate and the pipe channel layer.