Abstract: Through survey of present ecological security situation of the mountainous region in Three Gorges reservoir area of Chongqing，the reasons for threatening ecological security in Three Gorges reservoir area are analyzed．It is pointed out that planting in steep slope，over reclamation and graze，excessive cutting firewood and utilization of land and biological resources ，vegetation distruetion，unsuitable development mountain areas and construction of factory and town，and untreated emision waste of work and living are main factors to threat ecological security of Three Gorges reservoir area ．The baekword production model，extensive cultivation and management，unsuitable structure of industry and So on make coelogical system further worsen． Finally，the countermeasures and proposes of establishing ecological security system including the accelerating natural protection region construction，putting small basin construction and stereoscopic agriculture construction into practice，and retuming the grainplots to forestry are put forward．