With the rapid development of cloud computing, the Internet of Things (IoT) and other new generation information technologies, a new service-oriented networked intelligent manufacturing mode—cloud manufacturing (CMfg), is emerged. In the CMfg paradigm, cloud manufacturing platform service innovation is an effective way to improve the service function, service quality and service efficiency of cloud manufacturing platforms. However, the service innovation of cloud manufacturing platforms is complex system engineering, which needs to consider many participants with independent interests simultaneously. If one party’s behaviour strategy changes, the whole system will be affected. In order to adapt the decision-making management of manufacturing service innovation in cloud manufacturing system, to provide the effective decision-making support for service innovation of cloud manufacturing system in uncertain environment, to explore the interaction mechanism and equilibrium strategy of various stakeholders in the evolution process of cloud manufacturing system. This research constructs a tripartite evolutionary game model among participants based on evolutionary game theory, Analyses the influence of participants’ strategy choices, The Cloud manufacturing platform’s service quality coefficients and users’ preference Coefficients on the equilibrium state stability of cloud manufacturing systems, and uses MATLAB software for numerical simulation. The results show that the evolutionary stability strategy of cloud manufacturing enterprises plays a decisive role in the service innovation of the cloud manufacturing platform. When cloud manufacturing enterprises choose a noncooperation strategy, the evolutionary stability strategy of the cloud manufacturing platform is innovation. When cloud manufacturing enterprises choose a cooperation strategy, the evolutionary stability strategy of the cloud manufacturing platform is affected by the platform’s service quality coefficient and the user’s preference coefficient, and both factors can promote the evolution of cloud manufacturing platform service innovation. The platform’s service quality coefficient has a threshold value, which depends on the relative size of benefits, costs and user’s preference coefficient generated by the service innovation of the platform. Therefore, in the cloud manufacturing mode, the cloud manufacturing platform must rely on different enterprises to provide their own innovation resources to realize the service innovation of the cloud manufacturing platform, so the cloud manufacturing platform should focus on introducing a group of high-quality cloud manufacturing enterprises for cooperation. In addition, users’ strong demand for high-quality services can provide sufficient impetus for cloud manufacturing enterprises to choose cooperation and cloud manufacturing platforms to choose innovation, which can not only encourage cloud manufacturing platforms to provide personalized services for users but also avoid the extra waste of resources.