The safe operation of natural gas long-distance pipeline stations is the critical link for its sustainable transmission. Therefore, station operation risk assessment and space-time expression in high consequence areas have become a critical problem that must be urgently addressed. The conventional way to assess the probability of gas pipeline failure cannot meet the requirements of the natural gas operating companies for the safety assessment of natural gas stations. Taking the example of the China–Myanmar natural gas pipeline branch station, based on the fuzzy fault tree model (FFT), a comprehensive pipeline safety evaluation method (CPSE-FFT) has been introduced, which evaluates the risk factor of pipeline operation in the station area and the social security risk brought by it. In this case study, the method is applied to a branch station of the China–Myanmar long-distance pipeline. In the results, the probability of pipeline accidents in the area of the station is 5.79×10−4 times/year, and six buildings with higher risk levels among the 37 buildings are also exposed on the risk distribution map. The overall social risk level is also expressed. CPSE-FFT is a practical, reasonable, and accurate assessment method that can quantitatively reflect the risks posed by the safe operation of natural gas stations. This method is suitable for most natural gas station risk assessments. The results of the risk assessment provide a reference for managers and decision-makers to reduce the risk of natural gas stations.