To address the issues of deteriorated water exchange capacity and localized seston depletion in the suspended raft mussel farming area of Gouqi Island caused by suboptimal layout design， which severely impacts mussel growth， this study employed the three-dimensional hydrodynamic model FVCOM coupled with a tracer module and a particle-tracking module to systematically evaluate optimization schemes for their effects on water exchange capacity， exogenous seston supply， and mussel condition index. The results revealed that under the current farming layout， periodic seston depletion occurs during neap tides in nearshore areas and the central farming zone， with the maximum water exchange time exceeding 30 hours. Single-factor optimizations， including removal of nearshore farming units， addition of trumpet-shaped channels， and optimization of raft orientation， reduced the area of low-seston zones during neap tides by approximately 30.3%， 48.4%， and 11.3% respectively while decreasing the farming area by 7.1%， 9.6%， and 0 compared to the current layout， significantly mitigating localized seston shortages. The comprehensive optimization scheme integrating all three single-factor measures reduced the total farming area by 13.7% compared to the current layout while achieving a 70% reduction in low-seston zones during neap tides and shortening the maximum water exchange time to less than 20 hours. This significantly enhanced the overall seston concentration and daily growth rate of mussels in the farming area. With increased average seston intake per mussel， the condition index across the entire farming area improved by 6.0%. The study demonstrates that the comprehensive optimization scheme effectively improves water exchange and seston replenishment in the farming area while reducing spatial disparities in mussel growth among different zones. This research provides scientific reference for the management of suspended raft mussel farming areas.