A memory system includes a non-volatile memory having a plurality of memory cells and a memory controller. The memory controller is configured to generate a histogram indicating, with respect to each of a plurality of threshold voltage levels for multi-level cell (MLC) reading, a number of memory cells at the threshold voltage level, based on data read from the plurality of memory cells using a plurality of reference read voltages, estimate a plurality of read voltages for MLC reading of the plurality of memory cells as estimation values by inputting the histogram into a read voltage estimation model, determine, through MLC reading of the plurality of memory cells using a plurality of sets of read voltages, a set of read voltages for MLC reading as observation values, and update one or more parameters of the read voltage estimation model based on the estimation values and the observation values.