The Wenchuan Earthquake hit area, locating at the transition between Sichuan basin and Tibet Plateau, is one of most ecologically fragile regions in China, and is playing an important role in ecological security of Sichuan basin as well. The earthquake had not only caused huge human-being lost and property damage, but also had resulted in great impacts on ecosystems. Integrated remote sensing data and field survey, we have assessed the ecological impacts of the earthquake. The results suggested that: (1) 122136 hm2 of forest, grassland and wetland ecosystems were destroyed in the earthquake, and mainly distributed in 10 counties, such as Wenchuan, Pengzhou, Mianzhu. (2) 65,584hm2 of giant panda habitat was lost in the earthquake, 5.92% of total panda habitat, (3) 94.64% of damaged ecosystems were distributed in the areas with earthquake magnitude higher than VIII, 53.82% of damaged ecosystems in the areas with altitudes lower than 2000 meters above sea level, 66.09% of damaged ecosystems in the areas with slopes between 30-50°. Since the ecosystem damage resulted from the earthquake will threat ecological security of Sichuan basin, ecosystem restoration should be one of the main focuses in the context of earthquake hit area rebuilding plan.