In order to resolve the crisis of Confucianism, Xiong Shili consciously promoted the rational and philosophical transformation of Confucianism. When reconstructing the new ontology of Confucianism, he introduced rational thinking and combined it with traditional intuitive experience. He established the structure of "rational method → intuitive method", trying to resolve the contradiction between speculative method and intuitive method, use reason to ensure the universality of ontology knowledge. He advocates "rational knowledge → transcendent rational knowledge", and hopes to resolve the opposition between empirical knowledge, rational knowledge and intuitive knowledge and self-cultivation knowledge, use experience to ensure the objectivity of ontology knowledge. Xiong Shili's construction of "ontological epistemology" reflects the modernity of his modern confucianism thought, and can provide a reference for the discussion of Confucianism's participation in the construction of civilization in the scientific era.