In order to address challenges of safety analysis of global navigation satellite systems (GNSS) brought by its system of systems (SoS) characteristics such as complex relationships between its component systems, to identify and study the SoS safety hazards across-the-board, and to improve its safety and enhance the service, a GNSS safety modeling method was proposed in the base of the functional dependency network analysis theory from the view of SoS. The effects and reasons of hazards promulgation and random failures combination caused by complex relationships between component systems in GNSS were analyzed and investigated with some emphasis. The simulation results show that the method is able to describe the influencing process of hazards promulgation and failures combination clearly and conduct both orthodromic and antidromic reasoning analysis. The results also demonstrate the great potential and applicability of the method to SoS safety analysis of GNSS.