Nowadays, there are different kinds of public knowledge bases for cyber security vulnerability and threat intelligence which can be used for IoT security threat analysis. However, the heterogeneity of these knowledge bases and the complexity of the IoT environments make network security situation awareness and threat assessment difficult. In this paper, we integrate vulnerabilities, weaknesses, affected platforms, tactics, attack techniques, and attack patterns into a coherent set of links. In addition, we propose an IoT security ontology model, namely, the IoT Security Threat Ontology (IoTSTO), to describe the elements of IoT security threats and design inference rules for threat analysis. This IoTSTO expands the current knowledge domain of cyber security ontology modeling. In the IoTSTO model, the proposed multi-source knowledge reasoning method can perform the following tasks: assess the threats of the IoT environment, automatically infer mitigations, and separate IoT nodes that are subject to specific threats. The method above provides support to security managers in their deployment of security solutions. This paper completes the association of current public knowledge bases for IoT security and solves the semantic heterogeneity of multi-source knowledge. In this paper, we reveal the scope of public knowledge bases and their interrelationships through the multi-source knowledge reasoning method for IoT security. In conclusion, the paper provides a unified, extensible, and reusable method for IoT security analysis and decision making.