There are provided a 3-D semiconductor device and a manufacturing method thereof. The 3-D semiconductor device includes a substrate extending along a first plane defined by first and second x and y directions, the substrate having a pipe transistor formed therein, a plurality of word lines spaced apart at regular intervals along a third direction z perpendicular to the first and second x and y directions; a first vertical plug connected to a first end of the pipe transistor by passing vertically through the word lines; a second vertical plug, connected to a second end of the pipe transistor by passing vertically through the word lines; a bit line connected to a top surface of the first vertical plug; and a source line connected to a top surface of the second vertical plug, wherein the first and second vertical plugs have different size.