An encoding method for a memory storage apparatus adopting a Lien ECC scheme is provided. The memory storage apparatus comprises an ECC encoder using a Lien Code. The encoding method includes: receiving a write command comprising a write address and a write data; reading an existing codeword comprising a first flip bit indicating bit-flipping of the existing codeword and flipping bits of the existing codeword based on the first flip bit; encoding the write data into a new codeword based on a Lien Code by an ECC encoder, and flipping bits of the new codeword based on a number of bits required to be changed from the existing codeword to the new codeword; and writing the new codeword comprising a first flip bit indicating bit-flipping of the new codeword to the write address In addition, a memory storage apparatus using the encoding method based on the Lien Code is provided.