Modern time-of-flight mass spectrometer instruments exhibit excellent mass accuracy in the parts per billion range. At this level, mass calibration methods should consider potential distortions in the basic calibration. Factors which can cause distortions are to be under control. We have analytically modeled and numerically verified the influence of the main causes of mass calibration distortions, including the uncompensated dependence of flight time on the starting position, spatial gradient of the accelerating field, and overshooting at the rising edge of the accelerating pulse. Additionally, the relativity correction has been taken into account.