With the building and modernization of satellite navigation systems, compatibility analysis between them had become a more and more important issue. According to the crude compatibility methodology proposed by Unite States and European Union joint work group, a more accurate methodology was proposed in this paper by deriving more precise signal models, which considered real PRN codes and data rate. The effects of different signal parameters onto Spectral Separation Coefficient (SSC) were not the same. By the way of simulation, it was concluded that the effect of signal with short code and low data rate onto SSC was obvious, and the effects of signals from different satellites with same modulation onto SSC were almost identical. Finally, the intrasystem and intersystem interference between GPS and Galileo in LI was simulated. It was resulted that the major interference was GPS intrasystem interference in the case of receiving GPS C/A signals, maximum was 2.86 dB; the major interference was the one from GPS C/A signals in the case of receiving Galileo E1B signals, maximum was 0.364 dB. Moreover, the change of using MBOC as Galileo El Open Service signal instead of BOC(l,l) made the interference onto GPS LI C/A signal reduced by 0.207 dB.