In the phase retrieval process of partially coherent illumination for the transport of intensity equation method, since the CCD acquisition frequency is not synchronized with the LED emission frequency, which case the black and white stripes appearing in the phase retrieval result, as well as the phase result error caused by the acquisition angle deviation due to the mechanical movement and other issues, a registration progressive compensation algorithm is proposed. Firstly, the corner detection and cross-correlation matching are performed on the three intensity images with a certain angular deviation, and the error point pairs are removed to get the transformation matrix in order to correct the original deviation. At the same time, since the slow dynamic change of the illumination light wave is related to its low frequency component, initial compensation is performed in the new registration image to improve the illumination stroboscopic effect. Then, the initial phase of the sample is solved by using Transport of Intensity Equation. In order to resolve the halo that occurs at the initial phase edge, the phase is compensated for the highlighting of the vital sample information again. The real optical path system is built for experimental verification in this paper, and the results show that the proposed method improves the stroboscopic effect while correcting the angle deviation. In the experiment of microlens array, the relative error between the restored result and the actual result is 1.7%, which fully proves the correctness and effectiveness of the proposed algorithm.