Innovation management of infrastructure megaprojects is a challenging task. There are many risks in the process of innovation in engineering technology, such as shortage of funds, policy fluctuations, and difficulties in the transformation of achievements. Meanwhile, innovation organizations involve multiple participants, which makes cooperation complicated. Therefore, resilient innovation is proposed and considered as a tool that can optimize innovation management. The resilience of innovation depends largely on partnerships at the organizational level, which is rarely explored in current studies. This research aims to examine the relationship between organizational resilience and innovation network characteristics. Based on a survey of 164 participants in infrastructure innovation projects, the structural equation model (SEM) is used to explore the factors that influence organizational resilience. The findings show that there is a positive correlation between network characteristics and organizational resilience. Furthermore, the strength of network connections has a direct impact on the preventive and resistance ability of resilience. Network heterogeneity has an impact on the dual ability of resilience. Finally, a case study of the Qinghai-Tibet Railway innovation network shows that based on the above influence paths, we can find a strategy to reconstruct the network to improve resilience.