The successful use of inter-organizational information systems ( IOS) has become a key element in improving firm performance．In the process of IOS usage，systems，business process and management process are coordinated by the inter-organizational relationship and knowledge behavior．Based on the social capital and knowledge related theories，this study builds a theoretical model to explain how the social capital influences IOS assimilation．The hypotheses are tested using the partial least squares ( PLS) analyses method．The results demonstrate that the two important dimensions of social capital—structural capital and cognitive capital—affect IOS assimilation significantly，which are mediated by the process of knowledge acquisition; the other important dimension of social capital—relationship capital—is also important to IOS assimilation，but it is affected by the causal relationship of the three dimensions of social capital．Conclusion of this study will enrich the information systems assimilation theory，and guide firms to absorb IOS better．