With the rapid development of laser cooling technology，ultra-narrow linewidth lasers，and femtosecond optical frequency combs，the uncertainty and stability of laboratory optical clocks have now reached a level of small coefficients of 10^-18. Miniaturized，integrated，and portable optical clocks have unique advantages in next-generation“second”definitions，gravitational potential measurements，elevation difference measurements，and solid earth tide measurements. In the process of moving from the laboratory to practical applications，the control system needs to complete miniaturization and integration design without compromising performance indicators. During the operation of the optical clock，the dead time caused by the control system delay affects the system stability indicators of the transportable optical clock. To reduce the impact of dead time on the stability of the optical clock，a hardware platform is built using Xilinx's Zynq architecture chip as the processing core and embedded Linux system as the software core. An embedded control system for transportable ⁴⁰Ca⁺ ion optical clock is developed. Starting from the real-time interrupt requirements of the embedded control system of the ⁴⁰Ca⁺ ion optical clock，this paper analyzes the impact of the newly developed hardware platform on the timing delay during the operation of the optical clock. Through analysis，it is found that the impact of the control system on system stability is below 2×10^-16，which can meet the real-time requirements of the control system for transportable ⁴⁰Ca⁺ ion optical clock.