An auto-control system was designed and realized for the closed-loop operation of a strontium atomic clock. This closed-loop operation locked an ultra-stable laser to a frequency obtained by averaging two peaks of the spin-polarized spectrum of the hyperfine energy structure of an isotope of 87Sr. Firstly, the requirements for automatic control of the closed-loop operation of the 87Sr atomic clock were specified, including the controlling signals and their time sequences during laser cooling and trapping of the atoms, the detection of the clock transition spectrum, and the closed-loop operation. Secondly, these specified requirements lead to the design of the physical systems. Finally, the auto-control program was designed using LabVIEW, and data acquisition hardware from National Instruments. The measurements of the frequency stability demonstrated that the in-loop frequency instability is approximately 5×10-15/τ1/2, and the frequency instability for 3 000 seconds of sampling time is 5.7×10-17. These results demonstrate that the designed auto-control system meets the requirements of a strontium atomic clock for closed-loop operation.