Based on the current fierce national innovation competitiveness, this paper analyzes the mechanism of industry-university-research institute alliance that can effectively promote national innovation competitiveness, and finds that there is a risk of stability in the industry-university-research institute alliance; The main factors influencing the stability of the industry-university-research institute alliance are extracted, which are divided into 4 first level indicators and 17 second level indicators; The fuzzy analytic hierarchy process (FAHP) is used to analyze and construct the stability test model of the industry-university-research institute alliance; Finally, taking a specific industry-university-research institute alliance as an example, the stability of the alliance is calculated, and the results show that the model has good practicability. The paper introduces FAHP into the stability quantification of industry-university-research institute alliance, and provides a new idea and method for the research in this field.