Multi-Agent Systems (MAS) make it possible to perceive, collect, share, consolidate and revise information from multiple smart devices through the design of smart objects as agents within the Internet of Things (IoT) systems. Although multi-agent systems and related tools significantly change the paradigms used in systems optimization, the existing literature on MAS is not sufficient to explain modern distributed computing methods describing enhanced collaboration of IoT devices. This article presents comprehensive research that explains how smart objects such as sensors, smartphones, and data centers in IoT will affect the system's performance if they are integrated with MAS technology. In this context, general information about MAS and IoT technologies, the importance of interoperability in MAS, and how multi-agent technology can be used for various purposes, from capturing sensor data to decision making, specific to manufacturing systems, are explained. Afterward, technical, semantic, syntactic, and platform interoperability approaches that will enable communication and interaction of smart objects in IoT systems and how MAS can contribute to the establishment of these collaborations are expressed. Finally, it is presented how agent-based interoperability models affect the system's performance with a centralized and decentralized approach, specific to the manufacturing sector. The research has revealed that multi -agent systems can be integrated into each layer of the IoT, and in this way, it can increase the effectiveness of IoT in many areas from information security to efficient use of energy, from routing to increase system efficiency.