A memory controller that controls a memory device including a memory block includes an initial program controller configured to control the memory device to program at least one or more monitoring memory cells from among memory cells respectively connected to monitoring word lines from among a plurality of word lines connected to the memory block, a pre-read controller configured to generate a shifting information of a threshold voltage distribution of the monitoring memory cells based on a result of reading the monitoring memory cells before a read operation is performed on the memory block, and a pre-program controller configured to control the memory device to perform the read operation after applying a pre-program voltage having a voltage level determined according to the shifting information to the plurality of word lines.