A method of operating a semiconductor memory device includes applying a program pass voltage to unselected word lines, applying a program voltage of a third level to a selected word line in order to raise threshold voltages of third memory cells, decreasing a level of the program voltage from the third level to a second level and discharging channel regions of second cell strings including second memory cells in order to raise threshold voltages of second memory cells, and decreasing a level of the program voltage from the second level to a first level and discharging channel regions of first cell strings including first memory cells in order to raise threshold voltages of first memory cells. The cell strings are disconnected from a bit line while a voltage level of the unselected word lines rises to a level of the program pass voltage.