Mixed Reality (MR) is an advanced technology designed to enhance users’ experience and perception of interactions with objects in both virtual and real worlds. MR has enormous potential for improving human-cyber physical systems (HCPS) in the manufacturing industry. The transdisciplinary engineering (TE) characteristics of this research emphasize integrating advanced patent mining techniques to trend analysis of innovative MR technologies and applications in the manufacturing. Despite the growing popularity of MR applications, trend analyses in this emerging technology have relied on qualitative literature reviews and insufficient patent macro-analytics. Therefore, mapping patents related to MR inventions provides technology experts with better insights of technology development in the manufacturing. This research consists of a thorough review of non-patent literature (NPL) for the construction of MR domain ontology and a systematic patent mining analysis, including patent map analysis, patent clustering, patent topic modeling, and trend analysis of MR applications. A total of 709 patents from the InnovationQ Plus patent database are systematically identified and analyzed for trend discovery. The key terminologies, top ten patent assignees, top five applicants’ country origins, top six Cooperative Patent Classifications (CPC), and seven technology clusters and topics are identified. These findings provide reliable MR-enabled HCPS suggestions for the manufacturing.