SCBIT is organized into 11 departments, Administration office、Biomedical Informatics research group、Functional Genomics research group、Systems Biology research group、Translational Medicine research group、Technology Support department、Call Center、SCBIT-Inforsence Joint Lab、Life Science Data Center、Software Development、Bioinformatics Application Software lab.

The directors of SCBIT must answer for the Board of Trustees. Currently, the Board members include Science Technology Commission of Shanghai Municipality, Shanghai Institutes for Biological Sciences, Chinese National Human Genome Center, Fudan University, Jiaotong University school of Medicine, Shanghai Institute of Pharmaceutical Industry, Shanghai Institutes for Biological Sciences, Shanghai Institute of organic Chemistry and Shanghai Center of Research and Development of New Drugs. The center’s expert Advisory commission and Academic committee are combined by some famous scientists; they carry on the consultation, appraisal to the center development strategy and major decisions.