A program method of a non-volatile memory device, the non-volatile memory device including a peripheral circuit region and a memory cell region including a cell substrate and a cell string having memory cells stacked perpendicular to a surface of a cell substrate, the method includes performing a first program phase including programming a first memory cell connected to a first word line and applying a first pass voltage to other word lines above or below the first word line, and performing a second program phase including programming a second memory cell being connected to a second word line closer to the cell substrate, applying a second pass voltage to a first word line group below the second word line and applying a third pass voltage to a second word line group above the second word line, the second pass voltage being lower than the third pass voltage.