In order to better control the cost of complex and difficult railway tunnels, the cost data of some tunnel projects are analyzed. It is found that the complex and difficult tunnel projects are always characterized by serious cost loss, serious loss of overlong construction period and regional loss.  And then, the main factors affecting engineering cost are summarized from 4 aspects, i.e. engineering technology, engineering economy, engineering management and macro policy. Finally, suggestions, i.e. adjusting the cost of project in construction according to laws and regulations, and avoiding signing contracts with unlimited risks are put forward.