A memory system and an operating method thereof are provided. The memory system includes a buffer memory storing a plurality of meta-slices constituting meta-data, and a memory controller marking meta-slices being updated, among the plurality of meta-slices stored in the buffer memory, as dirty meta-slices, generating journal data including update information corresponding to the dirty meta-slices, and flushing the journal data together with one of the dirty meta-slices to a non-volatile memory device.