The memory system has an overwrite operation and an operation control method thereof. A nonvolatile memory device has a plurality of memory blocks including a plurality of memory cells stacked in a direction perpendicular to a substrate. When data of memory cells connected to a word line of a selected memory block is read, the need of reclaim is determined based on an error bit level of the read data. In the case that memory cells having an erase state among the memory cells connected to the word line become a soft program state, the read data is overwritten in the memory cells connected to the word line of the selected memory block.