Abstract: Under the background of "Double First-rate" strategic plan, the number of highly cited papers has become the important index to measure the research level of a college. Most current researches have studied the hotspots of highly cited papers from the perspective of subject, with less focusing on the specific institution, comparing the highly cited papers with total papers to summarize their inside and outside features and rules. In order to fully understand the current situation of highly cited papers in Shenzhen University, and provide reference and suggestion on how to cultivate highly cited papers based on ESI and InCites database, this paper analyzed and compared the total highly cited papers in Shenzhen University based on ESI and InCites, with the articles and reviews in nearly 10 years in SCIE/SSCI, including the subject, research fields, high yield journal, high yield authors, co-operating institutions and funding institutions in detail. Based on this, it predicted the potential highly cited papers in Shenzhen University, and compared the other 12 local comprehensive universities and some typical universities in Guangdong province with Shenzhen University on the macro level. The results showed, the scientific research level in Shenzhen University was improving continuously, and the number of highly cited papers was also increasing year by year, while there were still some gaps compared with Shanghai University and Zhengzhou University. In addition to strengthening efforts in scientific research, Shenzhen University should strengthen international exchanges and cooperation, and library should provide targeted subject service combining with data analysis.