A rubidium atomic clock digital servo system based on second-order integration is proposed for the shortcomings of traditional rubidium atomic clock taming algorithm. It utilizes the characteristic of high first-order integration coefficient to provide fast control of crystal oscillator frequency. At the same time, second-order integration is used to reduce the additional phase difference caused by rapid changes in crystal oscillator frequency, so that the output phase of the crystal oscillator is basically consistent with the frequency integration of the rubidium atomic clock transition spectral line, thereby significantly improving the stability and timing accuracy of the rubidium atomic clock output signal. The results of simulation calculation and experimental verification show that through the adoption of rubidium atomic clock digital servo system based on second-order integration, the tame locking time of rubidium atomic clock is effectively reduced, and under the tame state of GNSS control, key performance of rubidium atomic clock such as timing phase accuracy, punctuality phase accuracy, frequency stability have ben significantly improved, which can effectively support the expansion and application of rubidium atomic clock in some systems that require rapid deployment and response.