Risk assessment is the key and core technologies ensuring IT system security. Based on the comprehensive analysis to complex information systems, this paper first summarizes the typical characters of complex information systems and then gives new risk factors that complex system need to face. Furthermore, a new risk assessment method is proposed to evaluate the complex information systems. The method takes full account of the effect of complexity of complex information systems in each process of risk assessment, and utilizes multi-level risk views to carry out in-depth analysis to the risk of complex system.