The invention provides a compensation method and device for time synchronization equipment, a storage medium and computer equipment thereof. The method specifically comprises: acquiring acquired frequency discrimination and phase discrimination data of a local oscillator crystal in the time synchronization equipment, acquiring an aging rate and frequency offset data of the local oscillator crystal, constructing an aging rate calculation table of the local oscillator crystal according to the aging rate and the frequency offset data of the local oscillator crystal, and when a time frequency reference source of the time synchronization equipment fails, performing frequency correction and phase modulation compensation on the local oscillator crystal according to the aging rate calculation table. In the whole process, considering individual difference of aging characteristics when local oscillator crystals in different synchronization equipment leave factories, frequency correction and phase modulation compensation are performed on the local oscillator crystal according to the aging rate calculation table of the local oscillator crystal, so that the influence of the individual difference of aging characteristics of the local oscillator crystals on the output time performance of the time synchronization equipment can be effectively compensated, the stability of time signal output ofthe time equipment in the timing phase is improved, and a good compensation effect is realized.