As an important emerging field of science and technology, smart factories have received attention from academia, industry, and the government. Currently, although some scholars have examined the research trends in the field of smart factories, we have not found any research on the analysis of the knowledge output of relevant organizations among smart factories. An urgent problem is whether cooperation between organizations with different characteristics will affect the overall development of intelligent factories. This study aimed to perform a comprehensive analysis of the knowledge content and structure of a smart factory and the characteristics of its knowledge production structure. We also evaluated whether the triple helix structure was stable, and whether the research topics of different issues were similar. The triple helix model was used to study three aspects of the knowledge structure of a smart factory: university, government, and industry. Furthermore, the research contents of different organizations were analyzed in detail using network analysis. It was found that research funding at the national level leads to a knowledge spillover effect. After 2015, a triple helix knowledge structure was formed in the field of smart factories, which maintained a certain stability until 2020. The output of triple helix cooperation research has a significant impact. University research focuses more extensively and intensively on technology, government research on macro aspects, and Industry 5.0 has become a hotspot in industry research. The government needs to provide new platforms to integrate and promote the development of smart factories.