The uncertainty of technology innovation results in high risk. It is very important to innovation success that enterprise systematically manage risks in the technology innovation process. The main task of risk management is to identify and evaluate all risks. In the article, the source of innovation risk is concluded technology risk, market risk, organizing risk and environmental risk. On the basis of grey system theory and AHP method, a grey hierarchy evaluation model is put forward to quantitatively evaluate innovation risks. The purpose is to help enterprise assessing risks and taking countermeasure to minimize the potential loss and increase the innovation income.