A memory system and an operating method thereof are disclosed. An operating method of a memory system including a nonvolatile memory device and a controller configured to control the nonvolatile memory device includes the controller updating original data of firmware stored in the nonvolatile memory device, the controller transmitting a notification signal, which notifies a host device of completion of the updating of the original data, to the host device when the updating of the original data is completed, and the controller updating backup data of the firmware stored in the nonvolatile memory device after the notification signal is transmitted.