Abstract: In response to the decline of offshore fishery resources, constructing marine ranches has become critically important. As core facilities in marine ranching, floating reefs can effectively restore pelagic ecosystems. However, existing floating reefs face the significant technical bottlenecks, such as short service life, high maintenance costs, and the risk of generating marine debris from structural fragmentation. Therefore, developing novel floating fish reefs that balance economy, durability, and ecological friendliness is essential for the sustainable development of marine ranching. This study proposed a novel structure composed of an underwater platform and multiple flexible floating units, aiming to develop a highly reliable, economical, and environmentally friendly marine ecological restoration facility. A time-domain coupled analysis model was established using three-dimensional potential flow theory, and its reliability was validated through a floating box mooring experiment. The study systematically investigated the structure’s dynamic response under varying wave conditions, and evaluated the stability of the remaining structure after the detachment of individual floating units. The results indicate that under varying wave periods, the surge, heave, roll, pitch, and mooring forces of each component of the flexible multi-body floating reefs exhibit periodic phase variations as the wave period increases. Furthermore, the surge, heave, pitch, and mooring forces demonstrate a positive correlation with increasing wave height. Upon the detachment of a single floating unit, the system’s motion response is significantly amplified compared to the intact state; the total amplitude increments for sway, heave, and roll of the underwater platform are approximately 0.43 m, 0.04 m, and 10.7°, respectively. Conversely, the peak mooring force coefficient of the main cable is reduced by approximately 8.6% compared to the intact system, indicating a certain degree of redundancy and replaceability of the floating units. These findings provide a theoretical basis and technical support for the engineering design and practical application of novel, eco-friendly floating reefs.