According to the theory of fracture, the influence of shearing force in Stress Intensity Factor on the crack section is taken into consideration, and corresponding theoretical formula are deduced in detail. Based on the complicated finite element model of dual-crack rotor system, the effects of crack depth and position on dual-crack rotor system is analyzed. Under different position assumption, the nonlinear dynamic response of rotor system with dual-crack in sub-critical, critical and supercritical zone are analyzed, and also the influence of different crack orientation on dynamic response of rotor system with dual-crack. The corresponding orbit of shaft center and frequency spectrum supply the theoretical reference to crack identification of cracked rotor system, especially to the rotor system with multi-crack.