Abstract: The "National Ecological Function Zoning"of China defined 50 national important ecological function areas, which have great significance on the protection of national and regional ecological security. Indicators were selected from two aspects of ecological stress and ecosystem structureto form ecological security evaluation system, and zoning ecological security evaluation based on remote sensing data of three periods were conducted on national important ecological function areas in order to identify areas where ecological security conditions show deterioration trends, which could provide theoretical and scientific basis for ecological security assurance of national important ecological function areas. Results show that ecological security indices of water conservation areas and biodiversity protection areas were relatively high, while soil conservation areas were in poor situation. Overall ecological security situation of national important ecological function areas has been declined. The ecological environment situation of Dongting Lake flood regulation areas and the southeastern Tibet mountain rainforest biodiversity protection areas improved significantly. While the ecological security index of the wind prevention and sand fixation areaslocated in the middle and lower reaches of Heihe River were the least and had a further declining trend.