The fuel assembly is the core component of the nuclear energy system, and its excessive deformation will affect the normal insertion of the fuel rod and endanger safe operation of the reactor. In this paper, we present an underwater fuel assembly deformation measurement system based on 10 sets of visual measurement units. Benefitting from the waterproof design, the shielding-radiation design, the reflective structure design, the dual-optical line laser triangulation principle, and the underwater multilayer refractive geometry, the measurement system has shorter measurement time, higher measurement accuracy, and better environmental adaptability. Through the underwater field measurement and verification of the standard rod and fuel assembly, the bow deformation measurement accuracy of the measurement system is better than 0.3 mm, and the twist deformation measurement accuracy of the system is better than 0.15°. The proposed method allows transient and high-precision measurement in a certain irradiation dose and certain depth water, which provides a strong guarantee for measurement of fuel assembly deformation parameters in deep water and high radiation.