A method of operating a memory system that comprises a memory device including a plurality of memory blocks and a memory controller, includes detecting a first memory block having a degradation count greater than or equal to a first reference value by the memory controller. A first command for the first memory block is transmitted to the memory device by the memory controller. A first voltage is applied to all of a plurality of word lines connected to the first memory block and a second voltage to a bit line connected to the first memory block in response to the first command by the memory device. The first voltage is greater than a voltage applied to turn on memory cells connected to all of the plurality of word lines. The second voltage is greater than a voltage applied to the bit line during program, read or erase operations.