Seagrass ecosystem is one of the most productive ecosystems in coastal waters providing numerous ecological functions and supporting a large biodiversity. However, various anthropogenic stressors including climate change are impacting these vulnerable habitats. Here, we investigated the independent and combined effects of ocean warming and ocean acidification on plant-herbivore interactions in a tropical seagrass community. Direct and indirect effects of high temperature and high pCO2 on the physiology of the tropical seagrass Thalassia hemprichii and sea urchin Tripneustes gratilla were evaluated. Productivity of seagrass was found to increase under high pCO2, while sea urchin physiology including feeding rate decreased particularly under high temperature. The present study indicated that future climate change will affect the bottom-up and top-down balance, which potentially can modify the ecosystem functions and services of tropical seagrass ecosystems.