Signal structure design is an important part of satellite navigation system research,which directly affects navigation performance.Signal performance parameters are analyzed and performances of BPSK modulated signals and BOC modulated signals are compared.Aiming at requirements of high navigation precision and high anti-jamming ability,a new navigation signal structure based on complex carrier modulation is proposed and performances of the signal are researched with different parameters.A synchronization algorithm is put forward according to the signal characteristics,and the synchronization performance is qualitatively analyzed.Next,the applications of the complex carrier modulated signal are discussed,which include anti-jamming,navigation enhancement,power combing and so on.Simulations and analysis show that the proposed navigation signal structure based on complex carrier modulation has good navigation capabilities and anti-jamming abilities,which deserves further study. Signal structure design is an important part of satellite navigation system research, which directly influence navigation performance. Signal performance parameters are analyzed and performances of BPSK modulated signals and BOC modulated signals are compared. Aiming at requirements of high navigation precision and high anti-jamming ability , a new navigation signal structure based on complex carrier modulation is proposed and performances of the signal are researched with different parameters. A synchronization algorithm is put forward according to the signal characteristics, and the synchronization performance is qualitatively analyzed .Next, the applications of the complex carrier modulated signals are discussed, which include anti-jamming, navigation enhancement, power combing and so on. Simulations and analysis show that the proposed navigation signal structure based on complex carrier modulation has good navigation capabilities and anti-jamming abilities, which deserves further study.