This paper investigates the impact of university-industry (UI) collaboration on firms' innovation efficiency using a balanced panel of 443 innovative firms in China from 2008 to 2011. An evaluation of firms' innovation efficiency shows that innovative firms do not show consistent performance across the two stages of the innovation process, namely, the R&D stage and the commercialisation stage. The empirical results demonstrate that UI collaboration can be detrimental to a firm's innovation efficiency initially but that the firm can benefit from UI collaboration as engagement deepens. In addition, UI collaboration affects innovation efficiency differently across the two stages once regional institutional factors are taken into consideration. Thus, pertinent policies may be required in order to facilitate UI collaboration and its role in improving innovation efficiency at different stages.