Low Density Parity Check (LDPC), as a type of advanced channel codes approaching Shannon limit, has been widely applied in the satellite navigation and communication fields. Modern GPS system has been adopted irregular LDPC codes to enhance the receiving performance of GPS L1C signal. Quasi cyclic-LDPC (Qc-LDPC) codes have the characteristics of simple structure, low decoding complexity and good performance of error correction. In this paper, the performances of two kinds of decoding algorithms of Qc-LDPC codes with different code length and different code rate are compared. The research results can be applied to guide the encoding and decoding design for different satellite navigation systems, such as GPS in USA, Galileo system in Europe and Compass system in China.