The invention discloses a deep space measurement and control system and a deep space measurement and control method on the basis of frequency-domain equalization and relates to the technical field of deep space measurement and control. The method comprises the steps that a ground station respectively carries out frequency spreading, constellation mapping and Fourier transform on measurement and control information and a time service code to generate two paths of frequency-domain signals, then forms time-domain signals after respectively carrying out oversampling, inverse Fourier transform and addition of a cyclic prefix on the frequency-domain signals, and transmits the time-domain signals; an aircraft obtains the measurement and control information, the time service code and two paths of m sequences; the aircraft processes the data information and the time service code to form a downlink signal and transmits the downlink signal; the ground station sequentially carries out time and frequency synchronization, channel estimation, removal of the cyclic prefix, Fourier transform, frequency-domain equalization and inverse Fourier transform on the downlink signal to obtain an equalizing time-domain signal and then carries out demapping and dispreading to obtain new data information and a new time service code; the ground station carries out phase comparison and calculates a distance. The deep space measurement and control system and the deep space measurement and control method have high resistance to multipath interference, can effectively improve a band utilization rate and solve the measurement and control difficult problem under the deep space remote low-elevation-angle condition.