A method of programming a nonvolatile memory device. The method may include pre-programming one memory cell among a plurality of memory cells by storing data in a first data storage layer using a first program voltage applied to one word line corresponding to the one memory cell among the plurality of memory cells; and while pre-programming other memory cells among the plurality of memory cells, background-programming the pre-programmed memory cell by moving the stored data to a second data storage layer using a second program voltage that is higher than the first program voltage applied to the word line of the pre-programmed memory cell.