Objective To systematically integrate and express knowledge from ancient materia medica literature dated before 1911 using ontology construction technology. Methods Utilizing content analysis, reusing existing ontologies in Traditional Chinese Medicine (TCM), listing concepts of materia medica knowledge, extracting relationships among concepts, constructing a knowledge framework, and adding concept instances. Protégé was used as the ontology construction tool, combined with Neo4j graph database for knowledge presentation and application. The quality of the ontology was evaluated by calculating coverage and consulting domain experts. Results An ontology for the materia medica field was constructed, including 21 concept classes such as names, classifications, and properties, and 15 relationships like equivalence, belonging, and treatment. The average coverage of the ontology framework terms was 90.72%. A knowledge graph prototype for the medicinal herb Eucommia was developed using this ontology, achieving visualization of the entity and relationship network in materia medica knowledge. Conclusions The constructed ontology integrates and reuses knowledge from ancient materia medica literature, demonstrating good consistency and term coverage. It can support the construction of knowledge bases and knowledge services in the materia medica field.