Collaborations between a focal firm and multiple universities or research institutes from diverse geographic regions have been a pervasive phenomenon in emerging economies. Drawing on the unbalanced panel data of 186 Chinese manufacturing firms listed on the main board, we examine whether and under what conditions industry-university-research (IUR) alliance portfolio concentration, the geographical concentration of IUR alliance partners, influence a focal firm’s innovation performance in emerging economies. The results suggest that IUR alliance portfolio concentration has a negative effect on firm innovation performance. Moreover, the negative effect of IUR alliance portfolio concentration on firm innovation performance is stronger for state-owned enterprises (SOEs) than that for non-SOEs. Besides, results also reveal that the negative effect of IUR alliance portfolio concentration on firm innovation performance is stronger for politically connected firms than that for non-politically connected firms. We discuss the implications of our findings for existing research on alliance portfolios and university-industry collaborations.