The nonlinear theory of large-orbit gyrotron traveling wave amplifier (gyro-TWA) was developed with consideration of misaligned electron beam. The effects of misaligned electron beam on both working mode and backward oscillation mode were studied using this theory. The results show that, for working mode, the average gain is decreased by the effect of misalignment, while for backward oscillation mode, the misalignment leads to changes of possible oscillation modes which makes the mode competition in large-orbit misaligned electron beam is more complex.