The rotor misalignment fault, which occurs only second to unbalance, easily occurs in the practical rotating machinery system. Rotor misalignment can be further divided into coupling misalignment and bearing misalignment. However, most of the existing references only analyze the effect of coupling misalignment on the dynamic characteristics of the rotor system, and ignore the change of bearing excitation caused by misalignment. Based on the above limitations, a five degrees of freedom nonlinear restoring force mathematical model is proposed, considering misalignment of bearing rings and clearance of cage pockets. The finite element model of the rotor is established based on the Timoshenko beam element theory. The coupling misalignment excitation force and rotor unbalance force are introduced. Finally, the dynamic model of the ball bearing-coupling-rotor system is established. The radial and axial vibration responses of the system under misalignment fault are analyzed by simulation. The results show that the bearing misalignment significantly influences the dynamic characteristics of the system in the low-speed range, so bearing misalignment should not be ignored in modeling. With the increase of rotating speed, rotor unbalance and coupling misalignment have a greater impact. Misalignment causes periodic changes in bearing contact angle, radial clearance, and ball rotational speed. It also leads to reciprocating impact and collision between the ball and cage. In addition, misalignment increases the critical speed and the axial vibration of the system. The results can provide a basis for health monitoring and misalignment fault diagnosis of the rolling bearing-rotor system.