Adopt software‐definition technology to decouple the functional components of the industrial control system (ICS) in a service‐oriented and distributed form is an important way for the industrial Internet of things to integrate information technology, communication technology, and operation technology. Therefore, this paper presents the concept of software‐defined control architecture and describes the time consistency requirements under the paradigm shift of ICS architecture. By analyzing the physical clock and virtual clock mechanism models, the global clock synchronization space is logically divided into the physical and virtual clock synchronization domains, and a formal description of the global clock synchronization space is proposed. According to the fundamental analysis of the clock state model, the physical clock linear filtering synchronization model is derived, and a distributed observation fusion filtering model is constructed by considering the two observation modes of the virtual clock to realize the time synchronization of the global clock space by way of timestamp layer‐by‐layer transfer and fusion estimation. Finally, the simulation results show that the proposed model can significantly improve the accuracy and stability of clock synchronization.