Abstract: The persistent decline of marine biodiversity, driven by synergistic global and anthropogenic pressures, highlights an urgent need to understand the functional roles of all ecosystem components—particularly overlooked rare species. Focusing on the depleted Zhoushan Fishing Ground in the East China Sea, this study applied a trait-based framework and conducted a virtual removal experiment to quantify the multifaceted impacts of rare species—identified using the Rabinowitz index—on fish community dynamics. Analysis of four seasonal surveys revealed that removing rare species consistently and significantly reduced total community biomass by an average of 6.76%. It also led to a substantial contraction in the community’s functional space (declines ranging from 14.92% to 34.77%) and a significant 5.20% reduction in functional redundancy, underscoring their critical role in expanding ecological strategies and enhancing functional insurance. Notably, while community stability increased significantly by 8.20% following rare species removal in spring 2025, changes in other seasons were non-significant, indicating temporally variable dynamics in which rare species can contribute to ecological variability. For methodological consistency and comparability of results, nonparametric statistical analyses were uniformly adopted for all four functional indicators (stability, biomass, functional redundancy, functional space): Kruskal-Wallis tests were used to examine overall seasonal variations, and Wilcoxon signed-rank tests to assess the significance of paired differences in each indicator before and after rare species removal. These findings clearly demonstrate the dual role of rare species: although their unique ecological strategies may introduce short-term fluctuations, they are essential for long-term resilience by uniquely supporting functional diversity and redundancy. This study provides robust empirical evidence that conserving rare biodiversity is not only ecologically meaningful but also a practical imperative for sustaining ecosystem multifunctionality and stability, offering a crucial scientific foundation for integrating rare species into ecosystem-based fisheries management in China and similar marine systems worldwide.