Yukawa Hideki was the first Nobel laureate in physics in Japan. He won the Nobel Prize in 1949 for creating the meson theory. He and his collaborators devoted most of the 1930s to the formation and development of meson theory, but from the 1940s, Yukawa worked toward his unified theory of elementary particles, including maru theory, nonlocal field theory, and field theory of elementary domains and particles. Although Yukawa’s theoretical research from the 1940s did not find general acceptance in the physics community, this exploration into the unified theory is deeply related to his main motivation for his lifelong research in theoretical physics, and it suggests his philosophy in theoretical physics. In order to understand his philosophy in depth, here we reconsider his research in his university years, which was the starting point of his theoretical research, and examine its relationship with the philosophy of Tanabe Hajime by using some of Yukawa’s archives in the Yukawa Hall Archival Library at Kyōto University. In addition, we will also review his writings relating to the ideas of Zhuangzi (Chang-tse), with which he was familiar throughout his lifetime, and examine the relationship between Yukawa’s theoretical physics and East Asian thought.