A semiconductor memory system and an operating method thereof include a memory device; and a memory controller including a sequence generator, a sequence analyzer, and a processor coupled to the memory device and containing instructions executed by the processor, and configured to generate a sequence by the sequence generator, wherein the sequence comprises a sequence of digital data, write the sequence associated with a user data to the memory device, read out a read data including the sequence and the associated user data, analyze the sequence to understand characters of the read data and create analysis result by the sequence analyzer, identify an optimal threshold voltage in accordance with the analysis result, and provide the optimal threshold voltage to an ECC engine.