High-speed rotary Fourier transform spectrometer has nonlinearity of optical path differences (OPD) because of refractor's rotating. Nonlinearity is an important aspect to be considered when material of rotor and scan angle are chosen. It is studied to direct engineering and more studying here. Its effect on interferogram and reconstructed spectrogram are discussed. Nonlinearity of OPD can cause variance periodic of interferogram. And it introduces noise and wave number shift of reconstructed spectrogram. Since OPD can be calculated while refractor rotating, Nonlinear OPD can be replaced with corresponding linear OPD in Fourier Transform to compensate the nonlinearity of OPD. The computer simulation testifies this method being effective. Noise caused by nonlinearity in reconstructed spectrogram disappears after being compensated.