This paper constructs an additive two-stage network DEA (data envelopment analysis) model with consideration of undesirable outputs and shared inputs. Following the triple bottom line standard of sustainability, we calculate both the overall and sub-stage sustainability performance of railway transportation in China from 2002 to 2013, from the aspects of economy, environment and society. The results show that the overall sustainability of China's railway presents a character of first declining, then rising and declining again. Moreover, the railway sustainability of China's eastern areas are much better than that of the western and central areas, and the gap has become much larger since 2009. As for the sub-stage efficiency, neither the production stage nor the service stage of the railway is efficient in sustainability, and the efficiency of the production stage is lower than that of service stage and plays a greater impact on the overall sustainability. Therefore, in order to improve the overall sustainability of China's railways, it is essential to improve the level of railway engineering construction and develop technological innovations in railway production.