The on-going paradigm shift knocking on the door of future wireless communication system is ubiquitous Internet of Things (IoT), and the maturity of which will be hindered by the challenges related to security. Artificial intelligence (AI) is proficient in solving intractable optimization problems in a data-based way, which provides a new idea for network security and physical-layer guarantee. In this paper, we divide the ubiquitous IoT networks into cyberspace and electromagnetic space, and identify the threat models. AI is analyzed from different taxonomies and application scenarios, then the technologies of it for ubiquitous IoT security are investigated from both the reactive and proactive perspectives. Finally, some imperative future directions are discussed.