There are many types of related data in laboratory work, complex inter-class connections, and various types of storage, which make it difficult for data integration and data-based scientific decision-making. At present, laboratory staff only have a preliminary understanding of digital management, but there is no clear idea and method on how to carry out in daily work. Starting from the laboratory data governance, a data governance method based on the knowledge graph technology is introduced, which is guided by the top-down knowledge graph construction strategy. Firstly, a conceptual model of laboratory management business and related data sets is constructed. Then, entities and relationships between entities are extracted from the existing business data, and the storage mode is optimized according to the actual situation. Finally, data storage is performed in the graph database. Through the experiment of this method, the laboratory data management is preliminarily realized, which lays a foundation for the subsequent data-based management.