Abstract: Multi-functionality in agriculture refers to the non-trade benefits of agriculture. In terms of WTO definition, this means benefits other than commerce and food production such as environmental protection, landscape preservation, rural employment, and food security. Due to specific natural conditions and human activities, agri-cultural heritage sites always have fragile ecological environments, rich cultures, undeveloped economies and multi-functionality. This implies that agri-cultural heritage sites have production, ecological, cultural and other functions. The concept of multi-functionality has triggered discussions on agri-cultural heritage systems in China and abroad. There are not only so lots of agri-cultural heritage systems in China but also long agricultural history, and most of which are under severe pressure of modernization and globalization. To promote sustainable agricultural development, international community has attached greater importance to conservation and utilization of agri-cultural heritages. Based on agri-cultural heritage systems and current state in China, this paper analyzed the value and significance of China’s main agri-cultural heritage and offered policy options for the conservation and utilization of agri-cultural heritage. The values of agri-cultural heritage systems in China were discussed from several aspects, e.g., conservation and utilization of traditional plants/animals, agri-technology, animal husbandry and medical technology, agri-customs and agri-landscapes. Based on analysis of values and significance, suggestions on conserving agri-cultural heritage system in China were proposed. These included: 1) establishment of the concept of “conservation” followed by the development of principles for dynamic conservation of agri-cultural heritage system; 2) strengthening of mechanisms and system building with specific attention on custody of agri-cultural heritage conservation and multi-participation system; 3) emphasizing conservation of agri-cultural heritage systems in Socialist New Countryside Construction; 4) building incentive mechanisms with visible importance of agri-cultural heritage system in harmonious community building; and 5) investing more conservation of agri-cultural heritage systems. All the above policy suggestions would foster the conservation and sustainability of utilization agri-cultural heritage system.