In the dual-camera phase retrieval method, the phase information is calculated by over-focus and under-focus images obtained through a single exposure after dual-cameras are installed on an inverted microscope. However, due to the processing error of the eyepiece and the installation error of the cameras, translation and rotation exist between the images, resulting in inaccurate phase retrieval results. In this regard, we proposed a dual-camera phase retrieval algorithm based on registration restoration and transport of intensity equation in this paper. Firstly, the defocusing image was registered. Then, image restoration was introduced to fill and restore the black cavity area caused by the registration. Finally, the transport of intensity equation under boundary conditions was used to acquire the high-precision phase retrieval results. The correlation coefficient of the simulation experiments reached 0.9309. In the experiment with a microlens array, the relative error between the restored result and the actual result was 2.8%, which proved the correctness and effectiveness of proposed method.