The rapid advances of China’s universities in major international league tables are generally believed to be an accomplishment of Project 985. A quasi-experimental study was, therefore, undertaken to test the belief and to evaluate the effectiveness of this policy intervention, using 15-year panel data between 1998 and 2013. Results from a difference-in-differences model showed that Project 985 had a positive effect on publication outputs of ‘985’ universities. Tier 2 ‘985’ universities gained strong momentum in publication growth in international and ISI journals. Additionally, Theil index decomposition was employed to examine the stratification effect of Project 985. Results confirmed the homogenising trend within ‘985’ universities. In contrast, the vertical differentiation between ‘985’ and ‘211’ universities was noticeably enlarged. While sustained public funding is still vital, the study findings inform policy makers and higher education leaders of greater sectorial and institutional reforms to fulfil individual higher education institutions’ needs and remove bottlenecks in publication growth.