The traditional grating fringe phase-shift method requires at least three grating images to extract the phase, which increases the measurement system's frequency and the image preprocessing workload. The Hilbert transform is used in a two-step phase-shift method to solve these problems. The Hilbert transform has the properties of a 90° phase shift and the ability to filter out the direct-current component. The phase extraction formula is used to calculate the phase after the grating fringe image has been processed by Hilbert transform. The nonlinear effect of the measurement system will distort the fringe images and the calculated phase will be inaccurate, which lead to the low accuracy of the final three-dimensional restoration. In the two-step phase-shift method, the formula of phase error caused by the nonlinear effect of the system is deduced, and the phase is iteratively compensated to weaken the influence of the nonlinear effect. The feasibility of the proposed method is verified via computer simulation, and the proposed method is applied to the three-dimensional surface shape reconstruction of the rail surface, providing an effective method for measuring rail wear and surface defects.