In this work the current state of the problem, which consists in choice the rational model of academic-industry consortiums such as “University – IT-company” is analyzed. There is researched the existing variants of successful innovative collaboration of academic institutions and IT-companies in Ukraine and abroad. At the present moment a matter of choice of partnership models based on the development of multicriterion evaluation system for possible level of cooperation of universities and IT companies is unsettled. Incorrectly chosen model of collaboration can lead to loss of a significant amount of intellectual and/or material resources, decrease of educational qualification level of specialists, limited in the training. To solve this problem it is developed and researched the intelligent decision support system based on fuzzy logic with hierarchically-organized structure for choice the most rational model of academic-industrial consortiums such as “University – IT-company”. Testing of the developed decision support system proved its high efficiency, which is confirmed by the authors for solving practical problems of choosing the model of cooperation within consortiums such as “University – IT-company” and for solving different types problems of transport logistics.