Provided are a memory controller and memory system having an improved threshold voltage distribution characteristic and an operating method of the memory system. As a write request of data with respect to a first block is received, an erase program interval (EPI) is determined denoting a time period elapsed after erasure of the first block. When the determined EPI is equal to or less than a reference time, data is programmed to the first block based on a first operation condition selected from among a plurality of operation conditions. When the determined EPI is greater than the reference time, the data is programmed to the first block based on a second operation condition selected from among the plurality of operation conditions.