—Research and development (R&D) collaboration is an important source of innovation. Network researchers have identified the importance of network resources in a firm’s innovation performance. However, previous studies have largely focused on the ego network (i.e., a firm’s own network position). In this study, we adopt an alter network perspective and explore how the network position of a firm’s alter (i.e., R&D partner) influences the focal firm’s innovation process. Drawing upon social capital theory and the knowledge-based view, we argue that R&D partners’ superior network positions (e.g., structural holes and centrality) provide second-order social capital, and positively influence a firm’s innovation performance through increased knowledge spill-in (or incoming knowledge spillover). We also find that relationship duration between firms and R&D partners moderates the relationship between R&D network positions and knowledge spill-in in an inverted U-shape. This study highlights the impact of second-order social capital on a firm’s innovation process from a knowledge-based view. We suggest that firms leverage both direct and indirect network resources and consider the dynamics in their R&D partnerships to facilitate better knowledge flows in the focal firms.