To gain a deeper understanding of the adaptive strategies of the globally threantened seagrass Halophila beccarii in response to salinity, this study explored the effects of four salinity levels (0, 10 as the control, 20, and 30) on its functional traits using a controlled indoor ecological water tank system. The functional traits assessed included leaf thickness, leaf area, specific leaf area, leaf dry matter content, aboveground biomass, belowground biomass, and total biomass. The results revealed three key findings: (1) Except for leaf dry matter content, which showed no significant difference between the control and the treatment groups, all other functional traits exhibited significant variations across salinity levels. Leaf thickness, leaf area, and specific leaf area were significantly higher in the treatment groups than in the control, with exceptions observed at 0 salinity for leaf thickness and at 30 salinity for leaf area. Conversely, aboveground biomass, belowground biomass, and total biomass were significantly lower in the treatment groups compared to the control, and biomass declined progressively as salinity levels increased. (2) Salinity changes altered trade-off relationships between functional traits. Compared to the control, the trade-offs between aboveground biomass and traits such as leaf dry matter content, belowground biomass, leaf area, total biomass, leaf thickness, and specific leaf area were strengthened. This indicates that as salinity stress intensified, H. beccarii reallocated its limited resources to aboveground growth to optimize survival under stress. Meanwhile, trade-offs between leaf area and traits like leaf dry matter content, belowground biomass, leaf thickness, and specific leaf area were weakened, reflecting a shift in allocation strategies to balance light capture efficiency and resource utilization under changing environmental conditions. (3) Salinity had both direct and indirect impacts on the functional traits of H. beccarii. Salinity directly influenced key traits such as leaf thickness, leaf area, aboveground biomass, and belowground biomass. Indirectly, it modulated the interrelationships among leaf traits (e.g., specific leaf area, leaf dry matter content) and biomass, thereby affecting the overall performance and adaptability of the plant under stress. These findings highlight the complex interplay between salinity, functional traits, and resource allocation strategies in H. beccarii. By analyzing the functional traits and their trade-offs, this study provides new insights into how H. beccarii adapts to salinity stress, offering critical information on its ecological strategies. These findings are essential for understanding the mechanisms driving the decline of this endangered species and lay a scientific foundation for its conservation, management, and restoration. In particular, the study emphasizes the importance of maintaining optimal salinity conditions to support the growth and survival of H. beccarii, thereby contributing to broader efforts to preserve seagrass ecosystems globally.