In order to approach the theoretical limit of decode-and-forward strategy for the half-duplex relay channel, a cooperative LDPC coding structure and its corresponding optimization scheme is proposed. Different from the structure of Bilayer-Expurgated LDPC (BE-LDPC) codes, new structure makes the extra parity bits generated by the relay as a part of the overall code. Using the messages from both source and relay nodes, the destination node can decode the information of the source node. To analyze the performance of cooperative LDPC codes,bilayer EXtrinsic Information Transfer (EXIT) charts based on message-error rate is devised as an extension of standard EXIT. Based on bilayer-EXIT chart, a design methodology for cooperative LDPC codes is proposed, in which the degree distribution with maximum noise threshold is iteratively improved through Differential Evolution (DE). The experiment results show that the cooperative LDPC codes always outperform the BE-LDPC codes.