The Globally Important Agricultural Heritage Systems – established by the Food and Agriculture Organization of the United Nations in 2002 – is a certification expected to conserve traditional agro-ecosystems and associated biodiversity, natural resources, outstanding landscapes, and cultural heritages that are at risk of extinction in the current market system. Employing the Nishi-Awa Steep Slope Land Agriculture System in Tokushima Prefecture, Japan, designated as Globally Important Agricultural Heritage System in 2018, as the case study, this research explores the potential and contradictions of Globally Important Agricultural Heritage System to incorporate alternative values such as traditional knowledge, biodiversity, landscape, healthy diets, and cultural heritages into the dominant hierarchy of values that favor market competitiveness. Based on original field surveys, literature review, and qualitative analyses, the study demonstrates that while the Globally Important Agricultural Heritage System certification is expected to bring considerable economic opportunity through an increase in international tourists and price appreciation of the local agri-food products certified by a local agri-food labeling system (established by the public and private actors in the designated area), this system does not explicitly guarantee the values claimed in Globally Important Agricultural Heritage System certification. Therefore, the Globally Important Agricultural Heritage System scheme to conserve the claimed values in designated areas is faced with a contradictory situation in a market economy.