Network efficiency analysis becomes important in railways in order to contribute towards improving the safety and capacity of the rail network, making rail travel more attractive for passengers, and improving industry practice and informing policy development. However, a physical railway network structure is a complicated system, and the operation, maintenance, and management of such a network is a difficult task which may be affected by many influential factors. By using efficiency analysis technology for a railway network, combining physical structure with operation functions can help railway industry to optimize the railway network while improving its efficiency and reliability. This paper presents a new methodology based on complex network principles that combines the physical railway structure with railway operation strategy for a railway network efficiency analysis. In this method, two network models of railway physical and train flow networks are developed for the identification of key stations in the railway network based on network efficiency contribution in which the terms of degree, strength, betweenness, clustering coefficient, and a comprehensive factor are taken into consideration. Once the key stations have been identified and analysed, the railway network efficiency is then studied on the basis of selective and random modes of the station failures. A case study is presented in this paper to demonstrate the application of the proposed methodology. The results show that the identified key stations in the railway network play an important role in improving the overall railway network efficiency, which can provide useful information to railway designers, engineers, operators and maintainers to operate and maintain railway network effectively and efficiently.