Flange connection is widely used in aero-engine rotor system. The state of bolt is very important to the stable operation of the rotor, but the impact of bolt failure on the dynamic characteristics of the rotor system is not clear. Thus, the stiffness and geometry characteristics of flange connection with bolts failure and its influence on rotor dynamic response are studied. Firstly, a three-dimensional solid finite element model considering contact characteristics and a stiffness test device for flange connection with spigot are established. The stiffness characteristics and axis bending characteristics of flange connection after bolt failure are obtained by numerical simulation and experiment test. Secondly, the motion equation of the rotor with the characteristics of local stiffness asymmetric and initial bending result from bolt failure of the flange connection is established by a novel modeling method, and the dynamic response characteristics of the rotor are studied; Finally, a rotor test bench with flange connection is established to test the dynamics of the rotor when bolts fail, and its frequency spectrum and orbit characteristics are analyzed. The research results can provide a theoretical basis for simulation and identification of the bolt failure in rotating machinery system.