R&D cooperations with universities are key factors for innovative firms to get useful informationand knowledge for innovation from outside. However, there are high relational uncertainties inthe relationship between universities and firms because of the differences in their objects,missions, and cultures. The development of technology in its early stage or in generic knowledgealso causes high technological uncertainties in R&D cooperation between universities and firms. These technological and relational uncertainties are the main challenging factors for the firmswho are cooperating with universities, and therefore, it is crucial for the firms to strategicallycope with these challenges and to effectively manage the process in the implementation phaseof the cooperations with universities. Hence, this paper discusses two management systems, reciprocal adjustment system andcontrol system, which deal with these uncertainties and manage the implementation of R&Dcooperations with universities. Two management systems and their impacts on the innovativeoutputs of firms were analyzed. Technological uncertainties, relational uncertainties, and thecharacteristics of R&D cooperation between universities and firms were employed to discusstheir moderating effects on the relationship between each management system and firms'innovation outputs. According to the results, reciprocal adjustment system rather than control system has apositive impact on raising firms' innovation outputs in R&D cooperation with universities. Especially, two management methods, informal communication between managers of eachorganization and horizontal influence between partners, are considered crucial for enhancingthe performances of the alliances between firms and universities. When technological and relational uncertainties are high, reciprocal adjustment system exertmore influence on firms' innovation outputs than control system, and therefore, firms arerecommended to focus on reciprocal adjustment system. On the other hand, when technologicaland relational uncertainties are low, control system has more effect on firms' innovation outputsthan reciprocal adjustment system, and accordingly, firms are needed to concentrate on controlsystem. Firms are also guided to put emphasis on the optimal combination of reciprocaladjustment system and control system when the levels of uncertainties are different.