Structure and agency are important theoretical perspectives in the analysis of political issues. In the traditional sense, people have been using “rule by man” and “rule by law” to define the governance concepts of the two schools of Confucianism and Legalism respectively, but from the perspective of structure and agency, the opposition of the two governance concepts of Confucianism and Legalism is, to some extent, the dual opposition of subjective and objective, structure and agency. The legalists, represented by Shen Dao, showed the structuralism that paid too much attention to the structure and neglected the individual. Confucius inherited the cultural tradition of Zhou dynasty, his thought of “Ren” shows the emphasis on active individuals, and his thought of “Li” also shows he did not ignore the structure factors, but Confucianism developed into the intentionalism tendency that placed too much emphasis on active factors in Simencius School. After that, Xunzi tried to correct the bias by constructing “the unification of Li and Yi”, but he eventually fell into the pattern of Confucian political moralism. Han Fei, a master of pre-Qin legalists, showed his efforts to reconcile structure and agency by integrating “Fa, Shu and Shi” into his view of power, but eventually he became a deep structuralism. To some extent, the debate and development of the concept of governance of Confucianism and Legalism in the pre-Qin period were centered on the relationship between structure and agency.