Although many theoretical schools have been developed and thrived in the field of "geopolitics" in Western academia over the past 120 years, the influence of geopolitical research has been declining partly due to the lack of concern for realistic issues, which is embedded in its traditional research agenda. In China, geopolitical studies have mostly followed the Western approach until 2010 when a new "geo-setting" research agenda was launched. This geo-setting research agenda incorporates geographic knowledge and politics into the process of geopolitical analysis, which has demonstrated both theoretical and practical significance because it not only brings reform and innovation to geopolitical studies but also contributes to the promotion of the Belt and Road Initiative and the construction of a community with a shared future for mankind. This paper proposes a research approach and an analytical framework for nationa-state based and integrated interdisciplinary geo-setting studies, according to previous academic findings on geo-setting, including conceptualization, leading elements, structure, and simulation. This framework is illustrated by a case study of Japanese geo-setting during the period of Tokugawa Bakufu. From an integrated interdisciplinary perspective, this paper unveils how the Japanese geo-setting had evolved under the combined effects of both domestic and international factors at multiple scales. It also sheds light on Japan's domestic and external policy formulation and changes during the period of Tokugawa Bakufu. Finally, three suggestions are put forward to strengthen the current nation-state based geo-setting research: (1) to continue to apply the interdisciplinary approach; (2) to highlight an integrated approach featured by multi-factor, multi-scale and long-term analysis; and (3) to pay consistent attention to long-term dynamic simulation.