The invention discloses a method and a system for realizing multi-point light focusing and light spot optimization at any position. The method for realizing multi-point light focusing and light spot optimization at any position comprises the following steps: under the condition that no samples are loaded, carrying out graded distribution phase modulation focusing on light beams, thus obtaining ideal focusing light spots; after the samples are loaded, enabling the light beams to be focused to a scattering medium, thus obtaining distortion scattering light spots; partitioning an image of a spatial light modulator, loading phase light focusing to each subarea, thus obtaining corrected scattering light spots, and carrying out once correcting cycle, thus obtaining new modulation phase distribution; loading the new modulation phase distribution to a spatial light modulator, carrying out modulation, carrying out light focusing again, thus obtaining the corrected light spots after the correcting cycle, and carrying out cross correlation calculation with the ideal focusing light spots, thus obtaining a cross correlation coefficient; and carrying out a plurality of times of circular correcting through iteration till the cross correlation coefficient after correcting cycle is greater than a preset coefficient threshold value. With the method and the system, the distribution of the scattering light spots is optimized, the limitation that the existing optogenetics photostimulation and microimaging scheme only can realize the stimulation at the single area is broken through, and the multi-area photostimulation and microimaging can be simultaneously realized under the great depth inside the brain.