Seagrass meadows represent one of the Earth's most valuable but threatened coastal ecosystems. The accelerating frequency and intensity of heatwaves and severe windstorms present unprecedented challenges to seagrass resilience globally. This study revealed that cumulative heatwave intensity, absolute temperature reached, and location within species' ranges serve as key factors mediating ecological impacts. Windstorms, including hurricanes, typhoons, and severe gales, threaten seagrasses through mechanical forces and sediment dynamics. At the ecosystem level, heatwaves and windstorms can trigger phase shifts where seagrass meadows transition to alternative states such as algal-dominated systems or unvegetated sediments. The vulnerability gradient across seagrass meadows depends substantially on their physical setting, and exposed and patchy meadows have much greater vulnerability to climate impacts than sheltered or continuous meadows. Therefore, effective conservation requires multi-scale strategies addressing both global drivers and local vulnerabilities. This study provides insightful approaches for advancing predictive capacity and conservation strategies for coastal ecosystem health.