The Internet of Things (IoT) extends the Internet connectivity into billions of IoT devices around the world, which collect and share information to reflect the status of physical world. The Autonomous Control System (ACS), on the other hand, performs control functions on the physical systems without external intervention over an extended period of time. The integration of IoT and ACS results in a new concept -autonomous IoT (AIoT). The sensors collect information on the system status, based on which intelligent agents in IoT devices as well as Edge/Fog/Cloud servers make control decisions for the actuators to react. In order to achieve autonomy, a promising method is for the intelligent agents to leverage the techniques in the field of artificial intelligence, especially reinforcement learning (RL) and deep reinforcement learning (DRL) for decision making. In this paper, we first provide comprehensive survey of the state-of-art research, and then propose a general model for the applications of RL/DRL in AIoT. Finally, the challenges and open issues for future research are identified.