To achieve the auto control of transition observation of the Optical Lattice Clock transition developed by the National Time Service Center, Chinese Academy of Sciences, a complete control system is designed. The control system consists of a timing sequence control unit with delay accuracy and synchronizing precision in μs level and a laser spectral scanning control unit. The two units were both realized through the virtual instrument exploited by LabVIEW software programming to control the optical field and magnetic field precisely. The two-level cooling and optical lattice trapping of strontium atoms are implemented and the high signal-to-noise ratio(SNR) clock transition 1S0-3P0 spectral line of strontium atom with a line-width of 180 Hz is obtained. The spectral line with higher SNR and narrower line width indicate that the optical lattice clock can operate in higher stability and whole control system meets the precision requirement of the running of strontium optical clock system. Moreover, the experiment demonstrates that the control system has universality, and can be extended to other systems to control the optical fields and magnetic fields.