Objective: To investigate the efficacy of intraoperative cognitive navigation on laparoscopic radical prostatectomy using 3D prostatic models created by U-shaped convolutional neural network (U-net) and reconstructed through Medical Image Interaction Tool Kit (MITK) platform. Methods: A total of 5 000 pieces of prostate cancer magnetic resonance (MR) imaging discovery sets with manual annotations were used to train a modified U-net, and a set of clinically demand-oriented, stable and efficient full convolutional neural network algorithm was constructed. The MR images were cropped and segmented automatically by using modified U-net, and the segmentation data were automatically reconstructed using MITK platform according to our own protocols. The modeling data were output as STL format, and the prostate models were simultaneously displayed on an android tablet during the operation to help achieving cognitive navigation. Results: Based on original U-net architecture, we established a modified U-net from a 201-case MR imaging training set. The network performance was tested and compared with human segmentations and other segmentation networks by using one certain testing data set. Auto segmentation of multi-structures (such as prostate, prostate tumors, seminal vesicles, rectus, neurovascular bundles and dorsal venous complex) were successfully achieved. Secondary automatic 3D reconstruction had been carried out through MITK platform. During the surgery, 3D models of prostatic area were simultaneously displayed on an android tablet, and the cognitive navigation was successfully achieved. Intra-operation organ visualization demonstrated the structural relationships among the key structures in great detail and the degree of tumor invasion was visualized directly. Conclusion: The modified U-net was able to achieve automatic segmentations of important structures of prostate area. Secondary 3D model reconstruction and demonstration could provide intraoperative visualization of vital structures of prostate area, which could help achieve cognitive fusion navigation for surgeons. The application of these techniques could finally reduce positive surgical margin rates, and may improve the efficacy and oncological outcomes of laparoscopic prostatectomy.