The College of the Environment and Ecology (CEE) at Xiamen University was established in March 2011 by integrating the discipline of Environmental Science from the former College of Ocean and Environment and the discipline of Ecology from the College of Life Sciences. The Ecology program was originated from the Department of Zoology and Botany established in 1922, and the Environmental Science program was originated from the Institute of Environmental Science established in 1982.

The College has three undergraduate majors in Environmental Science, Ecology, and Environmental and Ecological Engineering; five master's and doctoral programs in Ecology, Environmental Science, Environmental Engineering, Environmental Management, and Marine Affairs; and two postdoctoral training programs in Ecology, Environmental Science and Engineering . In September 2017, Ecology was selected as one of the national "double first-class" disciplines, and in 2020, Environmental Science and Ecology discipline was ranked the top 0.41% world-wide by Essential Science Indicators (ESI). In addition, Ecology and Environmental Science majors have been selected as national first-class undergraduate programs, and Environmental and Ecological Engineering major has been selected as a first-class undergraduate program in Fujian Province.