An operating method of a semiconductor memory device includes performing a first LSB program loop for storing first LSB data in first memory cells of a word line, performing a second LSB program loop for storing second LSB data in second memory cells of the selected word line and for detecting over-erased memory cells having threshold voltages lower than an over-erase reference voltage of a negative potential to raise the threshold voltages to be higher than the over-erase reference voltage, performing a first MSB program loop for storing first MSB data in the first memory cells, and performing a second MSB program loop for storing second MSB data in the second memory cells.