The Shanghai Astronomical Observatory is run under the system of director responsibility, in which the director is the legal representative of the organization, fully responsible for leading the observatory’s daily business and administrative operations. The organization is comprised of five managing departments: Main Office, Science & Technology Division (including Quality Division and Security Office), Personnel & Education Division, Finance Division, and Logistics & Infrastructure Division. These departments carry out the functions of the observatory jointly with three logistic support departments: Information & Computing Center, Office of Scientific Knowledge Dissemination, and Shanghai Astronomical Science & Technology Development Co., Ltd. The observatory has also set up an Academic Committee and a Degrees Committee for guiding and supervising academic research and graduate student education at SHAO.

        Presently SHAO has five research departments: Center for Astro-geodynamics, Research Center for Galaxy and Cosmology, Division of Radio Astronomy Science & Technology, The Astronomical Optical Instrument Group, and Time & Frequency Research Office. It also has five provincial-level key laboratories: CAS Key Laboratory in Galaxies & Cosmology, CAS Key Laboratory for Planetary Science, CAS Key Laboratory for Radio Science Astronomy (Branch), CAS Key Laboratory for Space Target and Debris Observation (Branch), and Shanghai Key Laboratory for Navigation and Positioning Techniques.