The emerging progress brought about by Industry 4.0 generates great opportunities for better decision making to cope with increasingly uncertain and complex industrial production. From the perspective of game theory, methods based on computational simulations and methods based on physical entities have their intrinsic drawbacks, such as partially accessible information, uncontrollable uncertainty and limitations of sample data. However, an insight that inspired us was that the digital twin modeling method induced interactive environments to allow decision makers to cooperatively learn from the immediate feedback from both cyberspace and physical spaces. To this end, a new decision-making method was put forward using game theory to autonomously ally the digital twin models in cyberspace with their physical counterparts in the real world. Firstly, the overall framework and basic formalization of the cooperative game-based decision making are presented, which used the negotiation objectives, alliance rules and negotiation strategy to ally the planning agents from the physical entities with the planning agents from the virtual simulations. Secondly, taking the assembly planning of large-scale composite skins as a proof of concept, a cooperative game prototype system was developed to marry the physical assembly-commissioning system with the virtual assembly-commissioning system. Finally, the experimental work clearly indicated that the coalitional game-based twinning method could make the decision making of composite assembly not only predictable but reliable and help to avoid stress concentration and secondary damage and achieve high-precision assembly. Obviously, this decision-making methodology that integrates the physical players and their digital twins into the game space can help them take full advantage of each other and make up for their intrinsic drawbacks, and it preliminarily demonstrates great potential to revolutionize the traditional decision-making methodology.