Provided herein may be a memory controller and a method of operating the same. The memory controller may include a command processor configured to generate a flush command in response to a flush request input from an external host and to assign a slot number corresponding to the flush command; a sequence generator configured to determine flush data to be stored in response to the flush command, and to generate a write sequence in which the flush data is to be stored based on a size of the flush data and an assigned device sequence of the plurality of memory devices; and a memory operation controller configured to control the plurality of memory devices to store the flush data in the plurality of memory devices.