A fast and simple solution is proposed to wavefront sensing for laser beams with spatial smoothly varying intensity, where Shack–Hartmann wavefront sensor and the modified Fourier domain centroiding algorithm are applied. Detailed analysis has been conducted to Fourier domain centroiding, simplifying the origin double-frame method to work with merely single frame, and revealing its interesting property of robustness to nonuniform intensity perturbation. The key parameter is also analyzed to optimize the algorithm’s performance. Numerical simulations demonstrate that the proposed method outperforms the center of gravity algorithm, with an average phase error reduction up to approximately one order in root mean square. Application of the proposed method in joint amplitude–phase compensation system is also verified by simulation with practical models and parameters. The modified Fourier domain centroiding is promising to enhance real-time actual wavefront measurement for adaptive optics in high-power lasers, such as joint amplitude–phase compensation.