A memory apparatus and an operation method thereof are provided. The memory apparatus includes a plurality of multi-level cells and a controller. The controller encodes input data according to a target encoding code to generate a plurality of encoded subsets, and stores the encoded subsets into the multi-level cells. Thereafter, the controller could read data from the multi-level cells, perform an error correction procedure on the read data to correct and recover the read data as recovered data, and decode the recovered data according to the target encoding code. Consequently, sensing windows between threshold voltage distributions of the multi-level cells are expanded.