Abstract: Effective management of Important Agricultural Heritage Systems (IAHS) hinges on a comprehensive understanding of their complexity, reflected in multiple values. These values include, but are not limited to, ecological, social, and cultural values, thus entailing an integrated value typology and possible quantitative evaluation approaches, focusing on the complex and dynamic agro-systems with strategic significance to human development. It is necessary to apply this value typology to specific cases so that certain evaluation indices can be proposed and valuation methods tested to confirm their practical feasibility, and to identify any gaps between theory and practice. With this in mind, and for a better understanding of the multiple functions of the Xinghua Duotian Traditional Agro-system (XDTA) in Jiangsu Province, a Globally Important Agricultural Heritage System (GIAHS), this research assessed its values according to the value typology. For the first time, the value of a GIAHS site was assessed, and as a second part of the two-part series of value typology and evaluation of IAHS, this paper presented a core value distribution in order to promote multi-stakeholder participation in conservation and development of the heritage site. Based on the constructed value system of the IAHS, this paper selected indices relevant to the land use and ecosystems of the XDTA, and collected data from multiple sources including the literature, statistical yearbooks, and social survey. The existence value of this GIAHS in 2016 was assessed following appropriate calculation approaches based on previously proposed evaluation methods, which covered a direct market approach, alternative market approach, and simulated market approach. Most of these approaches were widely used and proved feasible in the evaluation of natural resources and ecosystem services. The results showed that the total value of XDTA in 2016 was 68.581 billion RMB Yuan, of which the carrier value was 36.309 billion RMB Yuan and the service value was 32.272 billion RMB Yuan. For the service value, the brand value was 11.174 billion RMB Yuan, the ecological value was 10.240 billion RMB Yuan, the product value was 7.257 billion RMB Yuan, and the value of science, technology, society, aesthetics, culture, history, and spirit summed up to 3.600 billion RMB Yuan. Therefore, as a GIAHS, XDTA is a multi-type value carrier, the value system of which can reflect the multiple functions and global significance of GIAHS. Carrier value is the base for other product and service values, and a wide range of ecological values and outstanding brand values were also identified. These results could be regarded as basis for targeted conservation and brand value promotion for local governors. The research process and the aforementioned results indicate that the proposed value typology system is applicable to certain heritage sites, with their specific features reflected and evaluated by carefully selected indices and a combination of evaluation approaches. Value composition and distribution can be manifested to support targeted conservation management and to further integrate protected area management. However, more accurate evaluation is highly dependent on the selection of indices and their evaluation, which is achievable by deeper research into the explanation and quantification of non-materialistic values. Through index system optimization and dynamic monitoring of heritage sites, it is possible to generate a consistent value database to assist in the sustainable management of the heritage.