A memory system may include: a first memory device including a first normal block and a first auxiliary block; a second memory device including a second normal block and a second auxiliary block; and a controller configured to operate the first and second memory devices in an interleaving scheme, wherein the controller: checks a first used area of a cache buffer when a first data is buffered which is the most recently inputted, programs the first data in the first or second auxiliary block without erasing the first data from the cache buffer, when the first used area of the cache buffer is smaller than a predetermined size, and programs a second data of the predetermined size, which occupies a part of the first used area of the cache buffer, to the first or second normal block with erasing the second data from the cache buffer, when the first used area of the cache buffer is equal to or larger than the predetermined size.