Abstract: [Purpose / Signficance] The current competition of comprehensive national strength relies more on fundamental research, and highly cited papers have important significance in the evaluation and analysis of fundamental research. Revealing the differences between China and USA in leading basic research from the perspective of highly cited papers, we provide basic data support for national scientific research management decision-making and institution building. [Method / Process] Based on ESI highly cited papers of China and USA, this article uses bibliometric methods and Y index to analyze the specific features and differences of China and USA among three dimensions—trends of publication, country cooperation and institutional output.[Results / Conclusions] The study shows that: (1) Overall, the highly cited papers of China is 2.99 times that of the American highly cited papers, but the gap is narrowing yearly. At the same time, the low citation frequency and the low proportion of highly cited papers are still the shortcomings that limit Chinese international influence. (2) China and USA are closely cooperating with each other. USA dominates scientific research cooperation, as the proportion of first authors and corresponding authors and leading papers is significantly higher than that in China. (3) Chinese high-output institutions have obvious advantages of corresponding authors, but the output gap between institutions is large. And the American high-output institutions are evenly distributed, and they are characterized by deeper and broader international cooperation and inter-agency cooperation.

Key words: ESI database, China, USA, highly cited papers, Y index, bibliometrics