This study is dedicated to the innovative research of smart factory operation management systems in the era of smart manufacturing. Against the backdrop of the rapid evolution of the information revolution, smart manufacturing, represented by a new generation of information technologies such as mobile Internet, big data, and artificial intelligence, is rapidly emerging. As an information-physical fusion system, smart factories interpenetrate physical and virtual resources by interweaving multi-scale production systems, forming an open, complex giant system with multiple levels and dimensions. It is found that smart factories face a complex and variable structure, and their production and operations involve a large number of cross-domain, cross-industry, and cross-region manufacturing resources, requiring the establishment of a new operation management system framework and breakthroughs in key theories and methods. This study provides comprehensive and in-depth theoretical and technical support for constructing a smart factory operation management system. It lays the foundation for the smart upgrading of the manufacturing industry.