Wheel wear is a natural phenomenon of wheel–rail rolling contact during vehicle operation. The non-uniform wear in lateral and circumferential directions is normally occurred on wheels. The lateral non-uniform wear will lead to the unexpected hollow wear which can cause flange to flange vibration at low-frequency band, and the circumferential non-uniform wear will result in the vertical vibration which is the originate from the polygon phenomenon. These two forms of wear are coupled to each other on wheels and affect the dynamic behaviours of wheel–rail system. In this paper, a wheel–rail contact dynamics model which includes the 3D geometric shape of wheel profile is established and employed to vehicle system dynamics. The results show that the contact mechanical properties of wheel–rail are greatly affected by the 3D wheel profile. The low-frequency vibration of wheelset caused by hollow wear and the high-frequency vibration by polygonised wear are coupled, which increase the vibrational acceleration of wheel–rail system and even made for the main problem of the periodic separation of wheel and rail and aggravate the wear of wheel polygon.