Different from previous studies analyzing the influence of network structure on actors’ performance by using a single network perspective, this article explores the impact of multilevel networks on innovation. Using a sample of 41,007 patents in the field of alternative energy of the USPTO database, we construct inventor collaboration networks at city and as well as country levels. In the empirical analysis, we use panel data and negative binomial regression models with fixed effects. To keep our results reliable, we use an instrumental variables approach to solve potential endogeneity problems and perform a series of robustness tests. The results show that inter-country collaboration network structure moderates the relationships between inter-city collaboration network structure and innovation performance. Our findings show that when country's centrality and structural holes are high, the positive effects of city's centrality and structural holes on innovation performance are enhanced, and the negative effects of city's clustering coefficient are weakened. Implications of the findings for complex innovation network theory and innovation policies are discussed.