The invention relates to a magnetoencephalogram system based on all-optical atomic magnetic detection and an obtaining method. An all-optical atomic magnetic sensor array is arranged on a flexible head-mounted sinking bottom plane; the flexible head-mounted sinking bottom of the all-optical atomic magnetic sensor array is bent along a detected head to form a helmet shape, and at least two reference magnetic field sources are arranged at the known position of the head; reference magnetic field source signals are transmitted to a space coordinate real-time analysis module to be processed to obtain real-time space reference coordinates; meanwhile, brain magnetic field information is then transmitted to a head external magnetic field analysis module to be processed; a magnetoencephalogram synthesis module performs real-time position positioning and repeated detection information fusion, and high signal-to-noise ratio brain magnetic field distribution is obtained. The system has the advantages that the method is simple, the structure positioning requirement is low, the system is easy to realize, sensitivity is high, the real-time performance is good, the reliability is high, the needed space is small, and the flexibility is high.