A semiconductor memory device includes memory cell blocks having physical pages coupled to memory cells, peripheral circuits configured to program the memory cells or read data stored in the memory cells, and a controller configured to control the peripheral circuits so that a pre-program is performed to make memory cells in the memory cell blocks have threshold voltages higher than a set voltage by programming memory cells of the selected memory cell block, having threshold voltages lower than the set voltage, in response to an erase command. The set voltage is an intermediate threshold voltage obtained from the threshold voltages of the memory cells of the selected memory cell block.