Abstract: To conserve important traditional agricultural systems of global, the FAO initiated a global partnership on the dynamic conservation and adaptive management of Globally Important Agricultural Heritage Systems (GIAHS) in 2002. After more than ten years of development, China now has the largest number of GIAHS in the world, while at the same time faces the largest degree of pressure relating to the conservation and management of GIAHS. Scientific monitoring plays an essential role in the improvement of heritage management. Effective heritage monitoring can, not only highlight the conservation needs of the heritage site itself and the maintenance of its values, but also contribute to the sustainable development of the heritage site. However, monitoring of GIAHS in China is a relatively new enterprise and lacks the theoretical knowledge needed to support effective monitoring; not to mention the design and establishment of a GIAHS monitoring system at the national level. Therefore, this paper first fully reviewed the experience and practice of World Heritage monitoring, and then elaborated on the key issues of GIAHS monitoring, with reference to World Heritage, such as the concept and connotation, scope and content, and data collection and management. Based on these issues, this paper put forward a monitoring system for GIAHS consisting of a three-leveled monitoring network, a dynamic monitoring system, and a two-leveled inspection system. The dynamic monitoring system is the core part of the GIAHS monitoring system, comprised of monitoring scope, contents, methods, and data management. The scope of GIAHS monitoring was defined as the changes in agriculture heritage systems and their associated conservation and development measures. The contents of GIAHS monitoring included value changes in ecological conservation, economic development, social maintenance, and cultural heritage, as well as management measures in capacity building, publicity, demonstration, and diffusion. As these contents varied in time and space, GIAHS monitoring should be carried out at multiple levels, such as the annual report and the survey report. The three-leveled monitoring network and the two-leveled inspection system were the foundations of the GIAHS monitoring. Not only did the two approaches help form a monitoring and patrol mechanism combining active monitoring with passive supervision, but also help form a closed loop by monitoring data collection and evaluation results feedback, so as to greatly improve the scientificity and systematicness of the conservation and management of GIAHS. The established monitoring system can, not only enrich the theoretical knowledge relating to GIAHS monitoring and further promote the practice of GIAHS monitoring in China, but also help improve GIAHS monitoring across the world.