HIRFL-CSR is a new ion cooler-storage ring system in China's Institute of Modern Physics (IMP). This facility can accelerate all ions from protons up to the heaviest element, uranium, with variable energies for nuclear physics experiments, material irradiation research, and heavy ion particle therapy and so on. With the completion of this project, a new accelerator control system has been developed to accomplish the beam injection, accumulation, acceleration, extraction and manipulation. In this paper, the architectures of the HIRFL-CSR control system and timing system, the basic function of operation software, the data cycles of power supplies and the RF cavity are described in detail. Furthermore, to fulfill the requirements of special physics experiments and enhance the facility reliability, several operation software improvements, including eliminating the magnetic hysteresis effects, dipole magnets field slow feedback and super-period slow extraction, are also introduced in this paper. (c) 2012 Elsevier B.V. All rights reserved.