Abstract: A nonlinear dynamic model of rotor bearing system with bolted joint structure which considering the gyroscopic moment and the initial deformation due to the uneven preload of the bolts is built. The Newmark-β method is utilized to obtain the nonlinear dynamic responses, and the time-domain response, the bifurcation plots, the frequency spectra, the Poincaré maps are used to carry out the routes to chaotic motion of the rotor system with bearing clearance. And then the effects of the initial deformation and the bearing clearance on dynamic responses are analyzed. The results show that with the increasing of the initial deformation, the chaotic motion of the disk at low speed is suppressed when the bearing clearance is present, the rotational speed from the quasi periodic motion into the chaotic state increased, the amplitude of the response near critical speed increased and the routes to chaotic changed; With the increasing of the bearing clearance, the motion state of the system is chaotic under a low rotating speed when the initial deformation is present. And the speed from the quasi periodic motion to chaos motion state is decreased. The results can provide a theoretical foundation for the design of bearing rotor system with bolted joint structure.