Ontological knowledge graph (OKG) is a well-formed visual representation that depicts knowledge organization in formal elements (e.g., entities and attributes) and their interrelationships. OKG is crucial for innovation management analysis as it provides a clear boundary to understand complex knowledge domain in detail. In the patent analysis field, it facilitates the definition of a well-defined patent portfolio, aiming for accurate and complete patent retrievals and subsequent analyses. In recent decade, the rapid growth of the information and communication technology (ICT) sector has rendered data centers (DCs) indispensable for data processing, storage, and cloud computing, while ensuring security and privacy during DC operations. However, their energy-intensive operations pose challenges to global efforts toward achieving net-zero emissions goals. In response, this research develops a formal OKG refinement process and uses DC net-zero technology OKG as case study for in-depth OKG refinement and application in patent portfolio analysis. The net-zero DC domain covers five sub-technologies. Utilizing the proposed OKG refinement and patent portfolio analysis framework, the 1801 most recent decade’s patents related to relevant “DC net-zero technologies” are retrieved and analyzed. Particularly in this case, DC colocation and server-as-a-service perspectives are the newly discovered sub-domains for OKG refinement. Furthermore, the research also adopts the technology function matrix and technology maturity to assess current and future technology development trends, providing crucial insights supporting strategic innovation management.