A large cavitation water tunnel is an important experimental facility for hydrodynamic research. During long-term operation, structural deformation is inevitably induced by environmental temperature variations, hydraulic pressure loads, and equipment vibrations. As a result, the deformation affects experimental accuracy and operational safety. In this study, a structural deformation monitoring system based on strain sensing is developed. An optimized sensor network is adopted, in which high-precision strain gauges are installed at critical load-bearing locations. Meanwhile, a self-developed deformation inverse algorithm is integrated. Online monitoring of local deformation at key positions and overall thermal deformation of the tunnel is achieved. The operational stability and long-term continuous monitoring capability of the monitoring system were verified through a shaft rotational speed test and a 24-hour continuous drainage test. The results show that structural strain responses can be stably and continuously acquired, which are further utilized to calculate the corresponding deformation, thereby providing effective data support for safety assessment and operational condition analysis of large cavitation water tunnel facilities. This study can pave the way for the design of long-term deformation monitoring systems for similar large cavitation water tunnels.