Prefabricated construction (PC) is considered to be a low-carbon construction method. Implementing prefabricated construction projects (PCPs) requires multiple industry organizations to participate and collaborate. As different PCPs are initiated and implemented, industry organizations will gradually gather into a complex and evolving collaborative network at the industry level based on specific collaboration relationships with different project backgrounds. The evolution of the collaborative network is related to how industry organizations interact with each other, and how PC-related knowledge and innovation has spread among organizations in the long term. However, the laws of network evolution and the micro effects that drive network evolution are still unknown. This study analyzes 236 prefabricated construction projects (PCPs) in Shanghai during 2015–2023, using the stochastic actor-oriented models (SAOM) method to explore how the macro structure of project-based inter-organizational collaborative networks for prefabricated construction (PC) technology implementation evolves over time, and how micro effects jointly support the evolution of the networks. The macro-level descriptive analysis of the network indicates that the collaborative network has become increasingly dense over time and continues to show a core–peripheral structure, with a small number of super-connected organizations. The micro-level SAOM analysis further reveals that the evolution of the collaborative network structure is driven by structure-based preferential attachment and geographic proximity effects, as well as attribute-based ownership similarity effect. This exploratory effort applies a network dynamics model to investigate the micro mechanism of the evolution of inter-organizational collaboration. The research results provide theoretical guidance and decision-making references for PC industry organizations to develop efficient network action strategies. In addition, it can help industry managers to formulate appropriate network management strategies.