Military-civilian scientific and technological collaborative innovation (MCSTCI) is an important intersection of civil-military integrated development strategies and innovation-driven development strategies, and has become a brand-new model for Chinese key scientific and technological research. The selection of cooperative partner between military and civilian innovation entities is not only the primary segment to carry out MCSTCI activities, but also an important foundation for achieving complementary advantages and win-win cooperation. Therefore, on the basis of summarizing and combing the evaluation indicators, a partner selection model based on interval-valued intuitionistic fuzzy set multi-attribute decision-making is proposed. Firstly, we improve the traditional scoring function, and combine the new scoring function and entropy weight method to determine the weight of each evaluation indicator. Secondly, considering the impact of decision-makers’ risk attitudes, a method of transforming evaluation matrix based on hesitancy distribution is proposed. Finally, the grey correlation and TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) method is used to mark and rank the candidates, and the innovation entities with the highest score is selected as the collaborative innovation partner. An example of a military equipment manufacturing enterprise in Beijing for partner selection in order to carry out joint technological research on a certain anti-ship missile weapon shows that the model is more comprehensive and flexible in solving fuzzy multi-attribute decision-making problems, and can assess and select cooperative partners for MCSTCI scientifically and objectively.