Abstract: Confucianism has been subordinate to the Shinto or Buddhism thoughts since it was introduced to Japan, without gaining an independent position. It was not until the Edo period that Zhuzi Doctrine got supported by the Tokugawa shogunate due to its inherent political functionality and quickly emerged and broke up into several schools in the Edo period of Japan. In the same period, other thought trends, such as Yangming Doctrine, Kogaku, which rivaled Zhuzi Doctrine, also rose in Japan. The ontology of different schools pertaining to Zhuzi Doctrine generally carries on the tendency of Zhu Xi's "essential idea" of "reason first and then the Qi". While the counter-Zhuzi Doctrine insists on the "Qi-monism" theory or the philosophical stand that the mind is the ontology. Generally, in recent centuries, the ontology thoughts of different schools of Confucianism in Japan reflect the monism tendency of attaching importance to the whole and having innate transcendence, which is inherited from the Confucianism in the Song and the Ming Dynasty. In the later Meiji period, this feature, in combination with German idealism, formed the idealism tradition in Japanese philosophy.