A memory system includes a nonvolatile memory device having a first data area storing M-bit data using a buffer program operation and a second data area storing N-bit data (N being an integer larger than M) using a main program operation and a memory controller configured to control the nonvolatile memory device. When a main program operation using data stored at the first and second data areas is required, the memory controller calculates values indicating a performance of the required main program operation to be executed according to a plurality of main program manners, selects one of the plurality of main program manners based on the calculated values, and controls the nonvolatile memory device to perform the required main program operation according to the selected main program manner.