Based on the ontology molecule theory in semantic technology, the paper studies how to utilize the ontology molecules to describe and organize clinical knowledge of which the semantic contents change in different dimensions. It extracts knowledge from clinical data sources, constructs clinical ontology molecules and develops semiautomatic tools for database building. Also, it establishes the comprehensive application platform of clinical ontology molecule base, puts forward the organization and application method system of multidimensional clinical knowledge, designs and implements the dynamic visual system of clinical course and Clinical Decision Supporting System(CDSS).