An integrated navigation/communication signal is proposed in our previous work. It considered Cyclic Code Shift Keying (CCSK) as a communication signal combined with traditional Global Navigation Satellite System (GNSS) signal, further the optimized cyclic shift set for communication signal was designed. Based on the previous research, a fuzzy judging algorithm is proposed to acquire the integrated signal in this paper. This algorithm adopts segmenting correlation domain to improve the integrated signal transmission robustness. Moreover, in order to solve incompatibility problem between the integrated signal and binary communication system, a strategy for optimizing cyclic shift set basing on dual-thresholds is proposed, in which interleaving coding is used to resist interference. The fault-tolerant rate of proposed algorithm is improved by about 87% compared with traditional algorithms. Based on the compatibility, the Bit Error Rate (BER) of the integrated signal decreases obviously, and the reliability of the communication system is improved greatly, benefiting from that interleaving technology and error correction coding is applied.