A method of programming a nonvolatile memory device comprises performing a first program operation on first memory cells and second memory cells so that threshold voltages of the first and second memory cells have a first reference level lower than a first target level, the first memory cells having the first target level as a first target level, and the second memory cells having a second target level higher than the first target level as a second target level; performing a second program operation on the second memory cells so that the threshold voltages of the second memory cells have a second reference level lower than the second target level; and performing a third program operation on the first and second memory cells to have the respective target levels.