The present disclosure includes a memory system, a memory controller, and an operation method thereof. The memory system may cache a subset of all map segments in a mapping table indicating mapping information between logical addresses and physical addresses in a map cache, may select map segments on which locking is to be set from the map segments cached in the map cache so as not to be evicted from the map cache based on information on all commands received from a host during a set period of time, and may set lock flags for the map segments on which locking is to be set. Accordingly, the memory system may reduce the overhead occurring in reloading previously evicted map segments in the process of updating a mapping table, and may optimize update performance for a mapping table within a limit that guarantees caching performance to a predetermined level or higher.