Agri-cultural Heritage Systems (AHS) have not only various values but also important enlightening roles for modern agriculture. With agro-scientific and technological progress, the traditional agriculture that has lasted for thousands of years is declining gradually, thus is attached the importance of exploring and protecting our AHS. As a traditional agricultural system for 1300 years, the Honghe Hani Rice Terraces System (HHRTS) has many significant characteristics such as beautiful landscapes, distinctive rice varieties, ecologically clean agricultural production systems, systematic methods of managing water and soil and special ethnic culture. It was designated successively as a Globally Important Agricultural Heritage System (GIAHS) in 2010 and as a World Heritage (WH) in 2013. In this paper, taking HHRTS as an example, we analyzed the economic, ecological, aesthetic, cultural, and social values, as well as the research values, of the GIAHS. We conclude that the restrictions on increasing peasant earnings and improving their living standards are difficult with the low efficiency of traditional planting patterns and the single-industry structure of farming in rugged terrain. However, these restrictive factors are beneficial for developing some industries like green agriculture, organic agriculture or ecological food production because of the clean farmland environment. In the end, we propose the basic approaches to protect the Hani terraces agriculture system should include the local governments to encourage the development of ecotourism, organic agriculture and featuring agriculture by multi-mode economic compensation. It is very important for protecting terraces to coordinate benefits among corporations, governments and villagers by making reasonable policies of compensation.