Population growth, loss of biodiversity, and climate change necessitate a new vision for the future of both agriculture and biodiversity. In order to safeguard and support the world's agricultural heritage systems, in 2002 the FAO started an initiative for the conservation and adaptive management called Globally Important Agricultural Heritage Systems (GIAHS). Tourism is suggested as part of the future as it is considered to be an alternative income source that will not only promote local economic development, but also provide the opportunity for tourists to learn about agriculture and ecology. However, inappropriate tourism in GIAHS sites will bring impacts on local culture and living styles, which not only threatens tourism's sustainable development, but also has the potential to damage these unique agricultural systems. This paper proposes that agriculture-based tourism is suitable for GIAHS and that Multi-functionality of Agriculture (MFA) can be the link between agriculture and tourism. This study constructs the framework for tourism development in GIAHS through MFA and applies it to the four GIAHS sites in China. Referring to the quantitative assessment for MFA and a qualitative analysis of the relationship between agriculture and tourism, we can give advice on agricultural tourism development in GIAHS sites. This framework also offers a universal methodology that allows stakeholders to communicate about the multiple functions of GIAHS across scales.