A method of operating a nonvolatile memory device includes reading data stored in a main cell and a flag cell using a first read voltage, the nonvolatile memory device comprising the main cell for storing data including a least significant bit (LSB) and a most significant bit (MSB), and the flag cell for determining a program state of the main cell, determining a program state of the main cell based on the data read from the flag cell, reading data stored in the main cell and the flag cell using a second read voltage if a MSB page program has been performed on the main cell, and reading data stored in the main cell using a third or a fourth read voltage based on the data read from the flag cell using the second read voltage, if a threshold voltage of the main cell shifts.