The deformation state of fuel assembly is an important monitoring index during core operation. The deformation detection system of spent fuel assembly based on underwater binocular vision can not only obtain three-dimensional (3D) sizes of key parameters of spent fuel assembly, but also measure the overall outline of the assembly. Based on high temperature and high radiation characteristics of underwater large-scale target, an underwater binocular detection system based on 16 sets of camera units was developed. And the detailed design of its modules was given. By means of Harris feature point and regional grayscale cross correlation method, the fast stereo matching of binocular camera module with radiation noise was realized. According to the experiment results of simulated pool and nuclear power field,the local measurement accuracy of the system is better than 0.2 mm, and the global parameters satisfy the measurement accuracy of 0.5 mm. It can provide a powerful tool for the measurement of local deformation and bending parameters of underwater spent fuel assembly with high temperature and high radiation.