A method for performing data management in a memory device includes: receiving a set of data from a host device positioned outside the memory device; encoding the set of data according to a first sub-matrix of a predetermined parity-check matrix to generate a partial parity-check code; performing post-processing upon the partial parity-check code according to a predetermined post-processing matrix to generate a parity-check code of the set of data, where the predetermined post-processing matrix is not equivalent to any inverse matrix of a transpose matrix of a second sub-matrix of the predetermined parity-check matrix; and writing/programming a codeword of the set of data into a non-volatile memory of the memory device to allow the memory device to perform error correction when reading the set of data from the non-volatile memory. An associated memory device and a controller thereof are also provided.