The invention discloses a rubidium oscillator-based standard frequency and time adjusting method. After a rubidium atomic oscillator is selected as a reference frequency source, a field programmable gate array (FPGA) performs frequency doubling and frequency division operations on the reference frequency source to obtain a locally generated second pulse signal. The FPGA performs phase difference measurement operation on the intrinsic second signal by using an external input second pulse signal as a reference. The measured phase difference value is endowed to an internal specified register of the FPGA and transmitted to an advanced RISC machine (ARM) through a data bus. The RAM calculates the variation value of the phase difference of the intrinsic second signal and the external input second signal along the time, and calculates the frequency difference of the rubidium atomic oscillator and the external standard frequency according to the difference value. The frequency difference value calculated by the ARM is fed back to the FPGA through the data bus. The FPGA performs frequency modulation operation on the rubidium atomic oscillator according to the received frequency difference value so that the output frequency source of the rubidium atomic oscillator is synchronized to the superior time frequency reference. The method has the advantage of providing high-performance, high-stability and high-precision time signals.