Emerging technologies are characterized by the uncertainty of technology and market. Innovation subjects exchange various resources in an active or passive way, which promotes the cross-border integration among technologies and cross-border cooperation among enterprises. In this paper, a multi-layer network analysis model of emerging technology cross-border fusion is constructed, and the exponential random graph model is used to conduct cross-level empirical research on the mechanism of emerging technology cross-border fusion. The results show that technology diversity and proximity hinder cross-border cooperation, and technology heterogeneity promotes cross-border cooperation. The strength and breadth of relationships promote the cross-boundary integration of technologies, and the relationship dependence limits the cross-boundary integration of internal and external technologies.