Abstract: The relationships among social capital, cooperation, and innovative capabilities were investigated based on the investigation of domestic manufacture enterprises. The results show that social capital (structural) has directly impacted on the innovative autonomous capabilities, and has indirectly impacted on the innovative autonomous capabilities through inter-firm cooperation and university-firm cooperation. Social capital (cognitive) has directly impacted on the innovative autonomous capabilities and cooperative innovative capabilities. At the same time, social capital (cognitive) also has indirectly impacted on innovative autonomous capabilities and cooperative innovative capabilities through inter-firm cooperation. Inter-firm cooperation has a positive direct impact on two types of innovative capabilities, and university-firm cooperation has a positive direct impact on the autonomous innovative capabilities. Inter-firm cooperation plays an important role between social capital and innovative capabilities for enterprises. The conclusion might provide guidance for enterprises to promote the innovative capabilities.