The vibration propagates in a media such as a shaft in the form of elastic waves. The propagation characteristics of the waves are affected by the geometry of the media, the material properties as well as the cracks. The study to elastic waves propagating in a shaft with transverse cracks can help to detect them. The transverse crack possesses different crack modes due to different external loads. The influence of the crack mode, the location and the depth to the propagation characteristics is investigated in this paper. Firstly, the local flexibility coefficients with three different modes are deduced. And then, the transfer matrix of the elastic wave can be obtained. Finally, the influence of the crack mode, the location and the depth of the transverse crack as well as the rotating speed to the propagation characteristics is then studied, both in a numerical and an experimental way. It’s found that mode III is the most suitable mode in this paper, the location of the crack will make the stopbands fluctuating, the depth mainly affects the bandwidth of the stopbands, and the increase of the rotating speed will shift up the stopbands without changing their bandwidths.