The paper compares the agricultural heritage conservation schemes of China, Japan and Korea and, in particular, the national programs and their implementation under Food and Agriculture Organization of the United Nations (FAO)’s Globally Important Agricultural Heritage Systems (GIAHS). This comparison allows an understanding of the background of developments, designation criteria, application procedures and implementation structures of GIAHS and of the respective domestic programs in terms of the differences in national circumstances of Japan, China and South Korea. The sequence of implementation of GIAHS and the national program differs in each of the three countries. China introduced a national program after GIAHS designation, Japan has GIAHS but no national program, and Korea implemented a national program before its GIAHS designation. Thus GIAHS candidate sites in China and Korea are now selected from among their respective pools of national agricultural heritage sites. On the other hand, commonalities can be seen in the perspectives of the three countries with regards to agricultural heritage conservation through the common emphasis placed on the designation criteria: historical significance, cultural value, fostering partnerships, rural revitalization and biodiversity conservation associated with the agricultural heritage systems etc. Thus, the cooperation between China, Japan and Korea and the perspectives they have will contribute to proposals for improvements to the FAO designation criteria for GIAHS. These will be comprehensively applicable to both developing and developed countries.