This study aims to assess the ecological restoration effects of Vallisneria natans in a multitrophic level ecosystem. The water-purification effects of two hierarchical configuration modes of V. natans-Bellamya aeruginosa and V. natans-B. aeruginosa-Hyriopsis cumingii were studied. Results show that a V. natans and B. aeruginosa configuration ratio of 15:2 stabilizes water quality at Grade IV (TN ≤ 1.5 mg/L, TP ≤ 0.3 mg/L), and increasing B. aeruginosa density significantly reduces total phosphorus. The V. natans, B. aeruginosa, and H. cumingii configuration at 15:2:10 stabilizes water at Grade III (TN ≤ 1.0 mg/L, TP ≤ 0.2 mg/L), with a positive correlation between H. cumingii density and chlorophyll-a removal. Furthermore, the filtration and biocycling actions of B. aeruginosa (snails) and H. cumingii (mussels) significantly reduce levels of Total Nitrogen (TN), Total Phosphorus (TP), and Ammonium (NH4+-N) in water, thus enhancing the self-purification capacity of the water bodies. However, the bioturbation effect of H. cumingii can temporarily increase phosphorus release from sediments, leading to a short-term rise in TP concentration in the water. Overall, the study concludes that multitrophic level ecosystems are effective in purifying water quality and offer significant ecological restoration benefits. This research provides crucial data support for future construction and ecological restoration projects involving multitrophic level approaches in China’s rivers and lakes.