Provided herein may be a semiconductor memory device, a controller, and a memory system having the same. By means of a method of operating the controller of the memory system, the semiconductor memory device, which is included in the memory system and including a plurality of memory blocks, is controlled. The method of operating the controller may include sensing a power-on state of the memory system, and performing an erased block scan operation on the plurality of memory blocks using a scan read voltage, based on sensing that the memory system is in the power-on state. Each of memory cells in the plurality of memory blocks may store at least two bits of data, and the scan read voltage may enable an erase state and a program state of the memory cells to be distinguished from each other.