The invention discloses an adaptive optical focusing interference compensation method and system. Fluorescent light excited in a sample is received by a photomultiplier tube and the light intensity of a focusing center at this time is marked as a threshold; a digital micro-mirror device is arranged at a conjugate surface of a rear pupil surface of an objective lens, region division is carried out, each divided region reflects an incident light beam of the region to a side light path, so that the light after phase compensation can return to a front side light path and the light beams of other divided regions are kept to be unchanged; the photomultiplier tube records focusing center light intensities after light beam phase changes of the divided regions; the divided regions with the light intensities larger than threshold are marked to obtain a compensated divided region; and after the digital micro-mirror device loads the compensated divided region, the light beams are focused again and a light speckle with the higher central light intensity is formed in the sample. Therefore, on the basis of the optical interference principle, the quality of the focusing speckle inside the scattering medium can be improved rapidly; and a new idea is provided for the optogenetics and the living-body deep high-resolution optical microimaging technology.