A data encoding method, a data decoding method, and a storage controller are provided. The encoding method includes: obtaining a verification data corresponding to a raw data according to a write command; adding the verification data to the raw data, and obtaining a scrambled data accordingly; and performing an encoding operation on the scrambled data to obtain a codeword data. The decoding method includes: performing a decoding operation on a codeword data to obtain a decoded codeword data, and obtaining a pre-scrambling data accordingly; identifying a verification data and a raw data in the pre-scrambling data; identifying one or more first system data corresponding to the raw data according to a read command; and determining whether the raw data is correct by comparing the one or more first system data and the verification data.