Seagrasses maintain cellular water balance by regulating ion concentrations and accumulating organic osmolytes, enabling them to survive in the fluctuating salinity of intertidal environments. However, the molecular mechanisms underlying seagrass responses to salinity changes remain relatively understudied. To address this, we conducted a multi-omics analysis of Ruppia sinensis under low, moderate, and high salinity conditions to uncover the mechanisms behind its adaptation to salinity fluctuations. Our research revealed that the transition from low to high salinity significantly altered the physiological characteristics of R. sinensis. Simultaneously, the species enhanced its ability to cope with and adapt to salinity fluctuations by increasing antioxidant enzyme activity. Integration of multi-omics data further indicated that under high salinity conditions, R. sinensis synthesizes more flavonoids to bolster its adaptive capacity. Additionally, the phenylpropanoid metabolic pathway appears to play a crucial role in the response of R. sinensis to changes in water salinity.