Abstract: Science Citation Index (SCI), Engineering Index (EI) and Index to Scientific and Technical Proceedings (ISTP) are internationally distinguished retrieval systems which are globally recognized systems for statistical analysis of scientific papers. By means of these systems, and along with MEDLINE and CSTPCD (Chinese Science and Technology Papers and Citation Databases), the scientific papers of Shanghai Jiaotong University cited by SCI, EI, ISTP, etc. between 1999 and 2008 were statistically analyzed. It was found that during this period, the scientific papers of Shanghai Jiaotong University increased dramatically and the quality of the papers improved greatly. However, compared with Tsinghua University and Harved University, Shanghai Jiaotong University still has a long way to go in increasing both the quantity and the quality of scientific papers, thus, some suggestions were proposed.