An operating method of a memory controller configured to control a memory device including memory blocks each for storing a plurality of pages is provided. The operating method includes transferring a program command to the memory device based on a write request from a host, updating a valid page bitmap representing validity of a plurality of pages based on valid page information received from the memory device, calculating a fragmentation ratio representing a segmentation degree between at least one valid page and at least one invalid page of a memory block based on the valid page bitmap, determining source blocks among the memory blocks in ascending order of fragmentation ratios, and performing garbage collection on the source blocks.