An method of operating a memory system including a plurality of memory cells includes changing an operation mode at least some of the memory cells which operate based on a first operation mode to operate based on a second operation mode; and performing a change erase operation on the memory cells for which an operation mode is changed on the basis of a change erase condition when the operation mode is changed. When memory cells operate in the first operation mode, a normal erase operation is performed based on a first erase condition, and when memory cells operate in the second operation mode, a normal erase operation is performed based on a second erase condition. The change erase condition is different from at least one of the first and second erase conditions.