Abstract: Globally Important Agricultural Heritage Systems (GIAHS) sites, designated by the Food and Agriculture Organization of the United Nations (FAO), are typical Socio-Ecological Production Landscapes and Seascapes (SEPLS). They play an important role in many areas, including the inheritance and conservation of traditional knowledge, food safety, agrobiodiversity conservation, and climate change adaptation. In order to more effectively promote GIAHS conservation and management, this article constructed a "GIAHS Resilience Assessment Framework (GIAHS-RAF)" founded on a comprehensive discussion of the importance of assessing GIAHS sites and resilience concepts. This framework was based on the Resilience Assessment Framework of Socio-ecological Production Landscapes and Seascapes model (SEPLS Model) developed by a team including the United Nations University (UNU), and clarified the purpose and defined the evaluation and calculation process. We used the GIAHS-RAF to assess the conservation effectiveness of the first GIAHS site in China, the Qingtian Rice-Fish Culture System in Zhejiang Province (RFC), from 2004 (one year before GIAHS certification) to 2016 (11 years after GIAHS certification). The results showed that the overall resilience of "Longxian Village" (core area of RFC) in 2016 was weak, with the scores of five capitals being 0.75 (material capital), 0.63 (economic capital), 0.61 (human capital), 0.57 (social capital), and 0.38 (natural capital). Additionally, we found that despite diverse local resident incomes and a social and economic infrastructure that adequately met community needs, problems such as local species loss and resident dissatisfaction with food diversity still existed. Compared to 2004, the resilience of the system after 11 years of conservation was higher which implied that implementation of the GIAHS initiative had a positive effect on traditional agricultural system, especially the material and economic capitals. These results are consistent with existing research results and field investigations, proving that the GIAHS-RAF can be satisfactorily applied to the assessment of the conservation effectiveness of GIAHS sites and other agricultural heritage systems.