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Mankind has entered the information society, and information breeds risk everywhere. Information security risk assessment will play a crucial role, which is applied to the entire life cycle of information systems, an essential technical mean in determining information system security level and has a very wide range of applications. Improved principal component analysis (IPCFA) process is use to evaluate in the light of some steps reflecting main function indexes. Case study shows that some indexes are significant in analyzing and assessing main function indexes. Through analysis and assessment, it is concluded that, PCFA approves to be practicable. Using the risk assessment technology, the information assets with possible threat, vulnerability and necessary protection in enterprise information system are analyzed. Based on the risk assessment results, the targeted safety measures are taken, and the risk is transferred and reduced, which is controlled within an acceptable range.