Various embodiments generally relate to a semiconductor device, and more particularly, to a controller, a memory system and an operating method thereof. In accordance with an embodiment of the present disclosure, an operating method of a controller for controlling a nonvolatile memory device may include receiving a read command from a host; determining whether changed L2P map data corresponding to L2P map data included in the read command is registered in a dirty list; and performing, when the changed L2P map data is determined as registered in the dirty list, a read operation on the nonvolatile memory device based on the changed L2P map data among L2P map data included in a plurality of L2P segments.