The present invention relates to a method of operating a non-volatile memory device. In an aspect of the present invention, the method includes performing a first program operation on the entire memory cells, measuring a first program speed of a reference memory cell, storing the first program speed in a program speed storage unit, repeatedly performing a program/erase operation until before a number of the program/erase operation corresponds to a specific reference value, when the number of the program/erase operation corresponds to the specific reference value, measuring a second program speed of the reference memory cell, calculating a difference between the first program speed and the second program speed, resetting a program start voltage according to the calculated program speed difference, and performing the program/erase operation based on the reset program start voltage.