The development of electronic health records, wearable devices, health applications and Internet of Things (IoT)-empowered smart homes is promoting various applications. It also makes health self-management much more feasible, which can partially mitigate one of the challenges that the current healthcare system is facing. Effective and convenient self-management of health requires the collaborative use of health data and home environment data from different services, devices, and even open data on the Web. Although health data interoperability standards including HL7 Fast Healthcare Interoperability Resources (FHIR) and IoT ontology including Semantic Sensor Network (SSN) have been developed and promoted, it is impossible for all the different categories of services to adopt the same standard in the near future. This study presents a method that applies Semantic Web technologies to integrate the health data and home environment data from heterogeneously built services and devices. We propose a Web Ontology Language (OWL)-based integration ontology that models health data from HL7 FHIR standard implemented services, normal Web services and Web of Things (WoT) services and Linked Data together with home environment data from formal ontology-described WoT services. It works on the resource integration layer of the layered integration architecture. An example use case with a prototype implementation shows that the proposed method successfully integrates the health data and home environment data into a resource graph. The integrated data are annotated with semantics and ontological links, which make them machine-understandable and cross-system reusable.