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 first data or a second data which is one's complement of the first data; and performing an encoding operation based on the Lien Code by the ECC encoder. The encoding operation includes: if the first data is received, generating a first codeword according to the first data; and if the second data is received, generating a second codeword which is one's complement of the first codeword according to the second data. In addition, a memory storage apparatus using the encoding method based on the Lien Code is also provided.