Wavefront Coding (WFC) is an innovative technique aimed at extending the depth of focus (DOF) of optics imaging systems. In digital imaging systems, super-resolution digital reconstruction close to the diffraction limit of optical systems has always been a hot research topic. With the design of a point spread function (PSF) generated by a suitably phase mask, WFC could also be used in super-resolution image reconstruction. In this paper, we use a deep learning network combined with WFC as a general framework for images reconstruction, and verify its possibility and effectiveness. Considering the blur and additive noise simultaneously, we proposed three super-resolution image reconstruction procedures utilizing convolutional neural networks (CNN) based on mean square error (MSE) loss, conditional Generative Adversarial Networks (CGAN), and Swin Transformer Networks (SwinIR) based on mean absolute error (MAE) loss. We verified their effectiveness by simulation experiments. A comparison of experimental results shows that the SwinIR deep residual network structure based on MAE loss optimization criteria can generate more realistic super-resolution images with more details. In addition, we used a WFC camera to obtain a resolution test target and real scene images for experiments. Using the resolution test target, we demonstrated that the spatial resolution could be improved from 55.6 lp/mm to 124 lp/mm by the proposed super-resolution reconstruction procedure. The reconstruction results show that the proposed deep learning network model is superior to the traditional method in reconstructing high-frequency details and effectively suppressing noise, with the resolution approaching the diffraction limit.