GNSS (Global navigation satellite system) has shown its ability on the non-safety relevant applications in various applications. In railway domain, safety is the utmost conc, GNSS-based train localization unit is the carrier of safe localization. EN 50126 standard specifies the electric and electronic system performance requirements as Reliability, availability, maintainability and safety (RAMS). Safety performance characteristic is based on the reliability and availability analysis results. The formal method considering the risk identification and analysis is compulsory for the safety assessment. This paper provides the method for hazard analysis of the GNSS-based train localization function and further the hazard rate estimation of each hazard. The model-based approach using GNSS localization unit working principle is proposed to study railway localization behavior features. The hazard for the localization unit is formally stated, real collected data on circular test track in Beijing is studied using the proposed method. The result shows that the safety requirement of the performance can be transformed into safety integrity properly, the risks of GNSS in train station environment conditions are presented.