Abstract：This paper has discussed the change of cross-links’ numbers and PDOP values for the GEO,IGSO and MEO in the cases of different schemes by UHF signal and Ka signal aimed at the simulated constellation of BDS. Besides, some different cases of cross-link schemes have been designed. Using these simulated observations 60 days’ auto-navigation has been performed. The influence of the cross-link ranging mode and the cross-link configuration to the precision of auto-navigation has been analyzed. The results indicate that the corss-link ranging mode will not affect the precision of auto-navigation. But the cross-link configuration will influence the precision of auto-navigation in the order of centimeter. Therefore, while designing the inter-satellite cross-link, navigation’s precision, link’s load and construction cost should be considered in order to achieve the best result.