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The Internet of Things (IoT) has emerged as a technology capable of connecting heterogeneous nodes/objects, such as people, devices, infrastructure, and makes our daily lives simpler, safer, and fruitful. Being part of a large network of heterogeneous devices, these nodes are typically resource-constrained and became the weakest link to the cyber attacker. Classical encryption techniques have been employed to ensure the data security of the IoT network. However, high-level encryption techniques cannot be employed in IoT devices due to the limitation of resources. In addition, node security is still a challenge for network engineers. Thus, we need to explore a complete solution for IoT networks that can ensure nodes and data security. The rule-based approaches and shallow and deep machine learning algorithms– branches of Artificial Intelligence (AI)– can be employed as countermeasures along with the existing network security protocols. This paper presented a comprehensive layer-wise survey on IoT security threats, and the AI-based security models to impede security threats. Finally, open challenges and future research directions are addressed for the safeguard of the IoT network.