[Purpose/significance] This paper aims to build a model for benchmarking analysis of two institutions by using ESI and InCites databases. It provides a feasible approach for comprehensive, quantitative and public comparison and analysis of the international delivery performance of benchmarking institutions. [Method/process] We used the index provided by ESI and InCites, including Web of Science documents, citation times, category normalized citation impact. According to the different literature contribution, we proposed three new concepts, all documents, leading documents and not-leading documents. We put forward a new index—participation rate to measure the paper competitiveness of the agencies. We compared the general paper competitiveness, the affiliated author, the cooperative organization and the publication of journals of two universities. [Result/conclusion] In this paper, Web of Science documents are used to describe the quantity of the document issued by the organization. The category normalized citation impact and citation times are used to describe the quality of the document issued by the organization. For A university, the number of documents is dominant, and for B university quality is dominant. According to the author’s data analysis, B’s top authors of international publications have greater influence, ranking in the front row. According to the data analysis of the cooperation institution, the cooperation between the best cooperation institutions in B is more efficient, and the cooperation between the two sides makes the international ranking more advanced. It is the main reason for the quality of published papers of B university that the impact factors of the periodicals where papers of B university published are much higher.