In a method of programming a three-dimensional nonvolatile memory device, a program loop is executed at least one time, wherein the program loop includes a programming step for programming selected memory cells among the memory cells and a verifying step for verifying whether the selected memory cells are program-passed or not. In the programming the selected memory cells, a level of a voltage being applied to a common source line connected to the strings in common may be changed. Thus, in a program operation, power consumption which is needed to charge-discharge the common source line can be decreased while increasing boosting efficiency.