In recent years, with climate change, many agricultural systems are facing severe environmental stress, which are seriously threatening the food security and sustainable development of agricultural system. Although mainstream agro-system can effectively reduce the adverse agro-production effect rapidly by using modern technology, but many of them bring serious ecological crisis at the same time. For the sustainable development of agro-systems, the stress mitigation options must give full consideration to ecological protection. The Globally Important Agricultural Heritage Systems (GIAHS) sites, relying on its unique land use, water conservancy facilities, traditional crops, etc., form unique production system creating a better match with local natural conditions. Based on disaster mitigation system theory and practice, this paper analyzes environmental stress counter-measures of several GIAHS sites in China. The water requirement of millet, a drought-tolerant crop in Aohan Dryland Farming System (recognized as a GIAHS pilot site in 2012), has a better match with local water conditions. By reducing vulnerability of crops, agriculture survived healthily in semi-arid regions. Honghe Hani Rice Terraces System (recognized as a GIAHS pilot site in 2010), relying on the unique land and water use patterns, has successfully reshape disaster inducing environment, and effectively reduce the risk/effects of droughts. Besides, due to the high price, rich crop diversity and variety of income channel, the Agricultural Heritage sites can ensure the economic income and agro-system health when facing environmental stress. Stress counter-measures of traditional agricultural systems make full use of the regulation and spontaneity ability of the natural system, which is an important way to achieve sustainable development of ecological agriculture.