AbstractTo meet the requirement of product variety and short production cycle, reconfigurable manufacturing system is considered as an effective solution in addressing current challenges, such as increasing customisation, high flexibility and dynamic market demand. Dynamic factory layout design and optimisation are the crucial factors in response to rapid change in the mechanical structure, software and hardware integration, as well as production capability and functionality adjustment. Nevertheless, in the current research, the layout design for reconfigurable manufacturing systems is usually simplified with autonomous devices being regarded as 2D shapes. Issues such as overlapping and transportation distance are also addressed in an approximate form. In this paper, we present a novel multi-agent cooperative swarm learning framework for dynamic layout optimisation of reconfigurable robotic assembly cells. Based on its digital twin established in the proposed learning environment (constructed in Visual Components and controlled by TWINCAT), the optimisation framework uses 3D digital representation of the facility models with minimal approximation. Moreover, instead of using a traditional centralised learning manner, multi-agent system could provide an alternative way to address the layout issues combined with the proposed decentralised multi-agent cooperative swarm learning. In order to verify the application feasibility of the learning framework, two aerospace manufacturing use cases were implemented. In the first use case, the layout compactness is reduced by 3.8 times compared with the initial layout setting, the simulated production time is reduced by 2.3 times, and the rearrangement cost decreased by 33.4$$\%$$ % . In addition, all manufacturing activity within the cell can be achieved with a feasible robot path, meaning without any joint limits, reachability or singularity issue at each key assembly point. In the second use case, we demonstrated that with the proposed dynamic layout optimisation framework, it is possible to flexibly adjust learning objectives by selecting various weight parameters among layout compactness, rearrangement cost and production time.