Rail corrugation usually appears in the subway operation, especially in the egg fastener zone. In order to reveal the vibration character of structure that is caused by rail corrugation, the rail corrugation is measured in the subway typical sections of straight and curve lines and the common and egg fastener zone. The vibration accelerations of the track, tunnel, and ground are tested. The vibration magnitude and transmission characteristics of the structure are compared in the time domain and frequency domain. The influence of rail corrugation on acceleration vibration level and the vibration reduction effect of egg fastener is analyzed. The results show that: 1) the corrugation in the egg fastener zones increases the dynamic impact between wheel rail and the vibration acceleration of rail-track bed-unnel-ground; 2) the rail corrugation in the egg fastener areas makes the vibration level of the structure under rail larger than that of the common fastener sections, and the vibration reduction effect is difficult to achieve; 3) the rail corrugation in the egg fastener areas is more serious than the common fastener sections, especially in the lines of smaller radius curve, larger capacity and faster speed. The influence of rail corrugation should be taken into account in the selection of track.