Research excellence is one of the key missions of universities and an important engine for socio-economic development. However, the outbreak of COVID-19 has affected academic research in many ways. This study examines the impact of the COVID-19 pandemic on the research performance of science and engineering faculty members in China's top research universities. It is found that the pandemic caused a decline in the numbers and quality of published articles, and the effects persisted over time. The negative effect of the pandemic on research excellence was more pronounced in the older faculty groups and departments of science. In addition, the pandemic has harmed international research collaborations among academics, which is likely to obstruct research excellence in the long run. In the end, this paper proposes several policy recommendations to reinvigorate universities' capacity for research innovation in the post-pandemic era.