Objective To analyze the scientific paper publications during 2013-2015 in Beijing Institute of Ophthalmology (BIO), providing a reference for research administration. Design Retrospective study. Participants The Chinese and English scientific papers published during the period from January 1st, 2013 to December 31st, 2015, in which BIO was the first affiliation of authors. Methods A statistical descriptive analysis of the following data was performed, the publication journal type (SCI, Chinese Medicine Association series, core periodicals and non-core periodicals), impact factor (IF) level, the research types (classified as clinical research, basic scientific research and epidemiological research), research focus, the distribution of first authors, title and academic degree, the funding supports. Main Outcome Measures The number and nature of papers, the types of periodicals, the research types and focus, the first author’s age, title and degree. Results During the 3 years, in total 292 scientific papers from BIO were published, including 90, 92 and 110 papers published in 2013, 2014 and 2015 respectively. There were 120 (41.1%) articles published in SCI journals, 91(31.2%) in Chinese Medical Association series, 68 (23.3%) in core journals and 13 (4.5%) in non-core journals. The average IF of SCI papers was 3.0~3.1. The main type of the published papers was clinical study. The main research focuses were glaucoma and ocular fundus diseases. The majority of first-authors aged < 30 or ≥45-year-old. Those with a doctorate degree published the largest proportion of papers, in total 121 out of 292 papers (46.9%). The papers published by staff members with a master degree had the highest proportion of SCI (67.6%, 25 papers). Post-graduate students occupied the largest proportion of first-authors for all papers (82 papers, 31.8%), followed by staff members with a senior professional title (74 papers, 28.7%). Staff members with an intermediate professional title occupied the largest proportion of authors for SCI papers (28.7%，29 papers). Funding resources were reported in papers for 288 times, which mainly included the National Natural Science Foundation of China, Beijing Nova Program and Capital Funds for Health Improvement and Research. Conclusion The overall quantity and quality of scientific papers were steadily increasing, but lacking of the high-impact-factor papers. Staff members with a senior professional title were the main force in publishing scientific papers. The support of multi-resource funds, such as national research projects, boosts the publication.