The giant panda habitat of Baoxing County, located in the transition zone from Sichuan Basin to the edge of southeastern Qinghai-Tibet Plateau, is the critical and key ecological function areas. At present, the puzzled problems present that the whole ecological system was interrupted by ecological management from different local department policy and the long merits for protecting giant habitat was weaken by short-term economic profits from natural resources. Exploring marbles and constructing hydropower plants and the livelihood activities of residents in the world heritage protection zone threatened to the protection for giant panda habitats. The government and people have taken a series of measures in recent years to deal with conflict: setting up nature reserves, establishing ecological protection projects, speeding up adjustment of industrial structure and international cooperation. The development practice of Baoxing County over the years shows that it is a sustainable and effective measure to grow economy while simultaneously protecting the giant panda habitats through Integrated Ecosystem Management (IEM). However, giant panda protection is destined a protracted battle in economy development process.