The transition of China’s railways from aggressive expansion to sustainable development has sparked widespread discussions on green railways. Previous studies have primarily focused on the fundamental aspects of green rail design and construction. However, the green operation phase, one of the most critical stages in the entire lifecycle of railways, has been overlooked. This study used a mixed-method approach, combining systematic review and qualitative analysis, to identify significant environmental, economic, and social evaluation indicators for green railway transportation operations. Through an examination of 123 articles and interviews with four professors in academia, two Planning and Design Institute technicians, one government staff, and one railway practitioner, this study identified 17 key indicators associated with green operations in railways. The results showed that previous studies in the environmental aspect primarily focused on noise pollution, water pollution, solid waste, ecological conservation, and the use of construction materials. In the social part, the main concern is social equality. Green railway operations have the potential to impact social equity through the movement of people and goods, which makes accessibility a preferable evaluation measure. Regarding economic indicators, the influencing factors are more complex (such as regional GDP per capita), making it difficult to evaluate the effectiveness of green railway operations directly. We suggest the inclusion of more economic-related indicators that directly correlate with green operations in railways.