The present disclosure relates to a memory controller and a method of operating the memory controller. The memory controller controlling a memory device including a plurality of planes includes a central processing unit (CPU) generating a command corresponding to a request from a host, a command queue storing the command, counter logic assigning to the command, number information corresponding to an order in which the command is generated and flag information indicating a level at which an operation corresponding to the command is performed, and a command queue controller controlling the command queue to transfer the command stored in the command queue to one of the plurality of planes corresponding to the command on the basis of the number information and the flag information.