The bearing-rotor-gear system is an important mechanical component for transmitting motion and power. Due to the complex responses, the condition assessment of the transmission system becomes more difficult. Thus, a model of the bearing-rotor-gear system with a misaligned rotor is built for implementing the complex response analysis. The misalignment rotor is realized by offset connection of couplings, and the creative excitation force is transferred to the bearing inner ring through the rotor. The constructed model is checked by the corresponding experiment. From the simulation results, it is found that vibration responses are modulated by rotor frequencies, and there are rotor frequencies, harmonic frequencies of bearings, and gear pairs in the spectrum. When the misalignment defect is deepening, the high-order harmonic responses are excited. If the revolving speed increases, the modulation of the rotor frequencies is accentuated, the vibration intensity generated by gear pairs is attenuated, while the harmonic response and super-harmonic response of bearings can be suppressed, and the system vibrates mainly at the low-frequency band. When the load becomes higher, the amplitudes of the rotor frequencies, meshing frequencies, and defect frequencies are all increased.