Bolted joints are major components to connect the multiple stages of disks in the aero-engine, which directly influences the motion state of the rotor system. This paper studies the effect of some typical structure parameters on the time-varying bending stiffness of the bolted disk-disk joint through finite-element simulations. Based on the Lagrange’s equations, a two-node element used to represent the bolted joint is derived, which is called the joint element. Then, a mathematical model of the rotor system with a bolted disk-disk joint supported by ball bearings is established through the Timoshenko beam and the joint element. The dynamic model is numerically solved using the Newmark-β method. The largest Lyapunov exponent, three-dimension spectral plots, and frequency-response curves are employed to reveal the effect of the bending behavior on the rotor dynamics. Comparisons indicate that the structural parameter of the bolted joint has a slight influence on motion stability, critical speed, and amplitude corresponding to the critical speed. Finally, an experimental study is conducted through a bolted-disk joint rotor test rig with an electrical tightening wrench, showing that the increase of pre-tightening torque will lead to a decrease of the amplitude corresponding to critical speed due to the hardening effect. The modeling method proposed in the present work paves a way for modeling and analyzing of the rotor system with a bolted disk-disk joint.