The rapid improvement accuracy of the atomic frequency standard puts forward higher requirements for the measurement resolution of the atomic frequency standard comparison system. To overcome the defect that the single zero-crossing point detection is sensitive to noise in the traditional dual mixer time difference measurement method, a digital frequency measurement method is proposed. This method combines sinusoidal beat technology, multi-channel synchronous acquisition technology, and digital frequency measurement technology, and uses differential compensation of system error to realize the precision measurement of atomic frequency standard. The frequency measurement accuracy is less than 2.5 × 10⁻¹⁴ and the noise floor is better than 6.5 × 10⁻¹⁵/τ = 1 s. The system has a high frequency measurement accuracy and a low noise floor, which can realize the precise measurement of a highly stable frequency source.

In response to the need for on-orbit performance evaluations of atomic clocks in low-orbit spacecraft, we integrated the operational conditions of the atomic clock ensemble onboard the China Space Station with the dual-mixing time difference measurement payload. In addition, we proposed a dual-verification framework that consists of on-orbit and ground-based simulations. Furthermore, this study elucidates the coupling mechanism between the thermal environment encountered during the orbit of the space station and the performance fluctuations of atomic clocks and their corresponding on-orbit measurement systems. The experimental results revealed that the periodicity of the on-orbit comparison data was correlated with periodic variations in the thermal environment of the space station orbit. Specifically, temperature change resulted in a phase-difference fluctuation of 1.51E–11 °C, indicating that temperature control plays a pivotal role in improving the on-orbit stability of atomic-clock measurement systems. This study provides a reference for the temperature control of on-orbit measurement systems and the on-orbit assessment of atomic clocks in low-orbit spacecraft.