A method for encoding digital data with a low-density parity check (LDPC) matrix includes: indirectly storing a non-regular portion of the LDPC matrix by storing a plurality of indices corresponding to a plurality of non-zero sub-matrices of the non-regular portion, and by storing a plurality of distance/location parameters respectively corresponding to numbers of zero sub-matrices between adjacent non-zero sub-matrices of the non-regular portion or respectively corresponding to distances between adjacent non-zero sub-matrices of the non-regular portion; generating at least one address according to at least one distance/location parameter; accessing information bits corresponding to the address; and recovering at least one element of the LDPC matrix according to at least one index and the information bits to encode the digital data according to the LDPC matrix.