In 1958, the Biological Research Center, the Soil Research Center, and the Geographical Research Center of the Xinjiang Branch of Chinese Academy of Sciences were established; in 1961, based on the above three research centers and the Xinjiang comprehensive survey team of Chinese Academy of Sciences, etc., the Xinjiang Integrated Research Institute of Water, Soil and Biological Resources, the Chinese Academy of Sciences was set up, which became the first research institute on the fields of resources and environment in Xinjiang.
　　In 1965, the Institute was divided into the Xinjiang Institute of Biology and Pedology (renamed as the Xinjiang Institute of Biology, Pedology and Desert Research in 1974) and the Xinjiang Institute of Geography and Geology (restructured to become the Xinjiang Earthquake Team in 1970, and restored to the Xinjiang Institute of Geography in 1978).
　　On July 7, 1998, according to the strategic plan of the structural adjustment and the strategic decision-making of the construction of the national innovation system of the party committee of the Chinese Academy of Sciences, the Xinjiang Institute of Biology, Pedology and Desert Research and the Xinjiang Institute of Geography were merged and re-organized as the Xinjiang Institute of Ecology and Geography, the Chinese Academy of Sciences. The Xinjiang Institute of Ecology and Geography thereby steps into the new course of innovation.
　　In January 1999, the Institute entered the second batch of pilot units of the base-type institutes of the Chinese Academy of Sciences.
　　On July 2, 2001, the institute was formally approved into the pilot units of the knowledge innovation projects of the second phase of the Chinese Academy of Sciences.
　　In June 2005, the institute completed the assessment of second-phase innovation, comprehensively achieving its goals.
　　In June 2006, the research and assessment center of the institute fully affirmed the innovation work of the second phase, pointing out that we had unique subject characteristics, obvious regional advantages, evidently increased competitiveness in science and technology, and strong trend of development. Meanwhile, they affirmed that the third-phase innovation program of our institute is reasonable, well-targeted with practical measures to be taken. The XIEG formally entered into the innovation of the third-phase.
　　In 2008, the XIEG conducted a comprehensive self-assessment of the preliminary work of the third-phase innovation. The results showed that the 3 proposals suggested by the Chinese Academy of Sciences targeting the XIEG in the third-phase innovation have been initially realized.