During the thickness assessment of an optical flat with wavelength-tuning interferometry, the second-order harmonics generated by double reflection inside the optical flat and nonlinear wavelength tuning reduce the accuracy of interferometric assessment. In this study, a harmonic phase-iterative analysis was proposed for the thickness assessment with the elimination of the effects of double reflection and nonlinearity. The harmonic phase-iterative analysis was derived by combining the intensity signal, including the harmonic components, with the partial least-squares method. Then, the proposed iterative analysis was integrated with the harmonic convergence condition and the selected pixel technique to improve the computational ability of the phase-iterative analysis. For evaluation, a numerical simulation and experimental thickness assessment using wavelength-tuning Fizeau interferometer were performed employing a five-frame harmonic phase-iterative analysis. The standard deviation of the experimental thickness assessment was 2.561 nm, which was smaller than those by other phase-detection technique. Based on the simulated and experimental results, it can be seen that the proposed harmonic phase-iterative analysis could determine the target phase with enhanced computational ability and compensation for the combined error between the second-order harmonics and the nonlinearity of the wavelength tuning.