A method of operating a semiconductor memory device includes performing a first program loop including a first program operation and a first verification operation in order to store a lower bit data of n-bit data in memory cells coupled to a page, performing a subprogram loop for memory cells of an erase state, having threshold voltages lower than a target voltage of a negative potential, so that the threshold voltages of the memory cells of the erase state become higher than the target voltage, and performing a second program loop including a second program operation and a second verification operation in order to store an upper bit data of the n-bit data in the memory cells.