A memory device includes an alternating stack of insulating layers and electrically conductive layers. Vertical NAND strings are formed through the alternating stack, each of which includes a drain region, memory cell charge storage transistors, and a pair of drain select transistors in a series connection. A common bit line is electrically connected to drain regions of two vertical NAND strings. The drain select transistors of the two vertical NAND strings are configured such that drain select transistors sharing a first common drain select gate electrode provide a higher threshold voltage for one of the two vertical NAND strings, and drain select transistors sharing a second common drain select gate electrode provide a higher threshold voltage for the other of the two vertical NAND strings. The different threshold voltages can be provided by a combination of a masked ion implantation and selective charge injection.