A method of operating a semiconductor memory device includes performing an LSB program operation for selected memory cells while raising a program voltage, when the threshold voltages of some of the selected memory cells reach a target level, storing data, corresponding to a relevant program voltage, in a first flag cell, performing the LSB program operation for some of the selected memory cells, having threshold voltages not reached the target level, until the threshold voltages of all the selected memory cells reach the target level, and after the LSB program operation is completed, performing an MSB program operation for the selected memory cells by using a program voltage, set based on the data stored in the first flag cell, as a start program voltage.