Abstract: The bottom nozzle is a fundamental structural component that supports and positions the fuel assembly, playing a critical role in debris filtration and providing coolant channels. Under the fluid force of the coolant, debris in the reactor core will erode the cladding of the fuel rods, potentially causing damage to the cladding and leading to serious consequences. The most direct way to avoid abrasion caused by debris is to block them outside the fuel assembly. As the first barrier for filtering debris in fuel assemblies, enhancing the debris filtering performance of the bottom nozzle plays an important role in improving the safety of reactors. Adding a debris filtering metal mesh to the bottom nozzle is currently a mainstream practice. The debris filtering capability of the bottom nozzle depends on the size of the mesh openings. Its significant advantage lies in its simple structure, which facilitates manufacturing. However, the debris filtration capability is limited, as particularly elongated debris can often pass directly through the holes in the mesh. To improve the debris filtration performance of the bottom nozzle, a novel design methodology for the filtration structure of the bottom nozzle has been proposed based on topology optimization theory. Abandoning the conventional approach of using debris filtering mesh, this method employs a novel three-dimensional filtering structure that integrates function and structure. The issue of debris filtration is abstracted as a geometric constraint problem between debris and the filtration structure, thereby integrating it into the process of flow channel topology optimization to achieve comprehensive optimization of both filtration performance and pressure drop performance. Typical debris within the reactor were selected for the optimization design of the filtration structure. The pressure drop performance was analyzed using computational fluid dynamics (CFD) methods, and the filtration structure test pieces were fabricated via additive manufacturing. Debris filtration tests were conducted on debris of three different sizes to validate the filtration performance, including ϕ1.8 mm×10 mm, ϕ1 mm×8 mm, and ϕ8 mm×1.2 mm. The research results indicate that, compared to the original structure, the filtration performance for three types of typical debris is improved by 60%, 25% and 20%, respectively. CFD numerical simulations show that the pressure drop of the topology-optimized filtration structure is reduced by 27% compared to the original structure. The topology-optimized debris filtration structure achieves a significant comprehensive improvement in both filtration performance and pressure drop performance.