A method based on an iterative Fourier-transform algorithm (IFTA) with phase optimization for phase-only multilevel diffractive optical elements (DOEs) is presented. Phase optimization by minimizing the mean-squared error composed of an amplitude-weighted probability-density function is performed in the IFTA iterations to ensure that the wavefront difference is minimized and thus to improve the DOEs' performance. Using the proposed method, we obtained a small standard deviation of diffraction efficiency of 20 uneven-phase DOEs, showing that DOEs with high diffraction efficiency did not vary significantly with the initial conditions. The simulation results of even- and uneven-phase four-level DOEs designed by use of direct and stepwise quantization IFTA methods are compared.