In recent years, collaborative robots have become one of the main drivers of Industry 4.0. Compared to industrial robots, automated guided vehicles (AGVs) are more productive, flexible, versatile, and safer. They are used in the smart factory to transport goods. Today, many producers and developers of industrial robots have entered the AGV sector. However, they face several challenges in designing AGV systems, such as the complexity and discontinuity of the design process, as well as the difficulty of defining a decentralized system decision. In this paper, we propose a new integrated design methodology based on swarm robotics to address the challenges of functional, physical, and software integration. This methodology includes two phases: a top-down phase from requirements specification to functional and structural modeling using the systems modeling language (SysML); with a bottom-up phase for model integration and implementation in the robot operating system (ROS). A case study of an automated guided vehicle (AGV) system was chosen to validate our design methodology and illustrate its contributions to the efficient design of AGVs. The novelty of this proposed methodology is the combination of SysML and ROS to address traceability management between the different design levels of AGV systems, in order to achieve functional, physical and software integration.