This study describes collaboration between firms and different organizations as a process of knowledge sharing, integrating inter-organizational collaboration networks and knowledge networks into a unified framework. It analyzes the bilayer structure of collaborative innovation networks, namely, the firm-knowledge bipartite network. The study investigates the impact of firm knowledge characteristics (diversity and uniqueness) on breakthrough and incremental innovation within collaborative innovation networks. The research employs patent data from Chinese A-share high-tech manufacturing companies listed from 2000 to 2018 and verifies the related hypotheses using a negative binomial regression model. The results suggest that, within collaborative innovation networks, firm knowledge diversity has a negative impact on breakthrough innovation but a positive impact on incremental innovation. On the other hand, firm knowledge uniqueness plays a positive role in breakthrough innovation but a negative role in incremental innovation. This study extends the understanding of firm technological innovation by considering both breakthrough and incremental innovation as distinct behaviors, providing a new perspective on the mechanisms underlying different innovation behaviors. By adopting a multilevel network structure approach to collaborative innovation, it contributes to a deeper understanding of internal and external factors influencing firm innovation behavior and expands the application scope of social network analysis.