A controller, a memory system, and operating methods thereof are disclosed. A memory system includes at least one nonvolatile memory device and a controller configured to control the nonvolatile memory device. The at least one nonvolatile memory device includes a super block including a plurality of way interleaving memory blocks and each of memory cells included in the plurality of way interleaving memory blocks operates in a first mode which stores N-bit (wherein N is a natural number of 2 or more) data. The controller generates a reproduction super block by replacing at least one bad block among the plurality of way interleaving memory blocks included in the super block with a non-way interleaving spare block and sets each of memory cells included in the non-way interleaving spare block to operate in a second mode which stores M-bit (wherein M is a natural number smaller than N) data.