Based on the framework of “resources-capability-performance”, this paper quantified the synergy level of the incubation network innovation system in Beijing, Tianjin and Hebei, Yangtze River Delta and Pearl River Delta by using data from 2015 to 2019, and then constructing the dynamic spatial Dubin model, which is used to explain the influence and spatial spillover effect of incubation network innovation synergy on regional innovation efficiency. The results show that: (1) At present, the synergy level in most cities of the three major city clusters is still in the initial stage of development, and the synergy development of the incubation network innovation system within the city cluster presents a significant imbalance;(2) incubation synergy has significant positive effects and spatial spillover effects on regional innovation efficiency while government support has negative regulatory effect on the promotion of incubation network innovation synergy to regional innovation efficiency.In addition,there are obvious differences in impact intensity,spillover degree and regulatory effect among the three major city clusters.