Provided is a method of manufacturing a semiconductor device. The method includes forming memory cells which share a data storage layer; performing a first strong program operation on first memory cells, arranged in a checker board pattern among the memory cells; performing a first annealing process after the first strong program operation; performing a second strong program operation on second memory cells arranged in a reverse checker board pattern among the memory cells, and performing a slight program operation on the first memory cells; and performing a second annealing process after the second strong program operation and the slight program operation.