According to the requirements and characteristic of space communication, protograph low-density parity-check (LDPC) codes have been proposed by Jet Propulsion Laboratory (JPL), which have better performance than conventional LDPC codes. In this paper, we propose a joint optimization algorithm for protograph LDPC codes, aiming at lowering the error floor of protograph LDPC codes, while maintaining good perfor ance at waterfall region without increasing encoding and decoding complexity. Theoretical analysis and simulation indicate that the repeat accumulate (RA) and accumulate repeat accumulate (ARA) codes designed by using the proposed algorithm have a remarkable coding-gain, and a lower error floor, as compared with the conventional RA and accumulated repeat by-4-jagged accumulate (AR4JA) codes at the high SNR region.