The risk assessment of engineering project is an important basis for the risk management countermeasure in project actualization phase. This paper brings forward design discipline of risk assessment index system, and founds risk assessment index system of engineering project based on it. In view of the shortcomings of traditional fuzzy assessment, which are coarse quantification of qualitative indices and unconsidering holistic information in the assessing process, grey theory is introduced into risk assessment, and establishes comprehensive assessment models based on grey theory and fuzzy mathematics. The fundamental and calculation steps of this method is clarified, an actual application indicates that this model is valid and feasible. The method can combine qualitative analysis with quantitative analysis effectively and synthesize expert group opinions adequately, which provides a good way for risk assessment of engineering project, as well provides a mathematical tool of analysis on risk assessment for such projects with limited number of samples and amount of information.