Smile distortion caused by aberration of the optical system is the key factor that affects the spectral calibration of a white-light spectral interferometer. To improve the accuracy of surface metrology, this paper proposes a novel calibration approach based on a line-by-line method. An acousto-optic tunable filter(AOTF)is adopted for the wavelength scanning process during calibration. By fitting sufficient calibration data, a more accurate relationship between wavelength and pixel position can be obtained. The simulation results show that the accuracy of surface metrology has different sensitivities to the coefficients of the calibration equation, and that the effect of smile distortion becomes more severe as the optical path difference increases. The presence of smile distortion is confirmed in the calibration experiment of a home-built white-light spectral interferometer. Subsequently, a silicon wafer and a standard step of 1.806 ± 0.011 μm are tested using the calibrated metrology system. The measurement results demonstrate that the line-by-line calibration method performs well in correcting spectral distortion and can improve the measurement accuracy of surface profile.