To accurately and efficiently control the probing sequence of the Hg? microwave atomic clock, a highly integrated custom timing control system was developed. This system adopts a layered architecture design, in which the host computer software enables parameter setting and sequence configuration distribution. The embedded software, in real-time, parses the received instructions and generates high-precision operation sequences, ultimately driving peripheral devices to precisely execute the corresponding operations. It achieves flexible configuration and dynamic reconfiguration of the timing logic. Experimental results show that the sequences generated by the system are consistent with the theoretically designed sequences, enabling convenient and efficient timing control for double-resonance probing, Rabi probing, and Ramsey probing. The system provides a reliable timing control solution for the integrated research of Hg? microwave atomic clocks.