Startups lack resources and manpower to build internal capabilities to strengthen market competitiveness; external cooperation such as joint research and networking plays is important. In this study, we analyzed the effect of startups’ industry-university cooperation on organizational learning capability and innovation performance. Empirical results demonstrate the mechanism by which government R&D investment strengthens organizational learning capability and creates innovative results by promoting cooperation between startups and universities. First, industry-university cooperation strengthened organizational learning capability. An empirical analysis shows that startups increase internal capabilities through external cooperation. Second, startups’ organizational learning capability had a significant effect on innovation performance. We analyze how organizations with high learning capabilities positively develop corporate innovation performance by having a culture of discovery and sharing new ideas. Finally, industry-university cooperation had different effects on organizational learning capability and innovation performance according to the previous experiences of startup founders. In particular, small- and medium-sized (startup) businesses and individual-based experience groups positively affected the creation of organizational learning capabilities and innovation performance through industry-university cooperation. Small- and medium-sized businesses and individual founders have a relatively small cooperative network with the outside world compared to founders of large companies, universities, and research institutes; therefore, they strengthen organizational learning capabilities through cooperation with universities. This study demonstrates that government should create policy inducements for cooperation with universities to maximize the R&D performance of startups. Criticism exists that lending support to startups and universities will hinder innovation performance; nevertheless, government investment plays a role in expanding intangible resources such as accumulating technologies, fostering high-quality human resources, and strengthening innovation networks. Therefore, the government should appropriately utilize the its authority to strengthen investment strategies for startup growth.