Memory controller, storage device and operating method thereof

A storage device includes a memory device and a memory controller. The memory device includes a first plane and a second plane, each including data blocks configured to store user data, one or more replacement blocks configured to replace one or more bad blocks, and system blocks configured to store system information. The memory controller is configured to replace, when a bad block is detected in the first plane after all the one or more replacement blocks in the first plane are used to replace previously detected bad blocks, the detected bad block with a target system block selected among the system blocks in the first plane.