An operating method of a memory controller configured to control a nonvolatile memory device including a plurality of memory cells is provided. The operating method includes: programming evaluation data into desired memory cells among the plurality of memory cells; performing initial verify shift (IVS) charge loss evaluation on the desired memory cells after a time elapses from a time point when the evaluation data is programmed, the IVScharge loss evaluation including an operation of detecting threshold voltage variation of the desired memory cells over a period based on the time elapsed from the time point when the evaluation data is programmed; and storing a result of the IVScharge loss evaluation; and adjusting levels of a plurality of read voltages used in the nonvolatile memory device based on the stored result of the charge loss evaluation.