Risk analysis model is systematic and structural process that considers internal security problems and threat factors of the information systems to find optimal level of security control. But, the risk analysis model is just only defined conceptually and there are not so many empirical studies. This research used structural equation modeling(SEM) research methodology with rigorously validated research instrument. Based on results of this study, risk analysis methodology was proved to be practically useful in e-commerce environment. Factors like threat and control were significantly related to risk. In conclusion, the results of this study can be applied to general situation or environment of information security for analyzing and managing the risk and providing new approach to comprehend concept of risk in e-commerce environment.