The invention relates to a system and a method for reducing background noise in magnetoencephalogram detection. A magnetic sensor array layer is arranged at the outer side of a head-mounted flexible substrate; a brain magnetic field sensor array and an outer magnetic field sensor array are distributed on left and right hemispheres of the brain; a magnetic shielding layer is arranged outside the magnetic sensor array layer; and a neck ring of a wearable magnetic field sensor is arranged on the neck of a human body. reduction of the background noise in magnetoencephalogram detection is achieved by collecting and analyzing a brain magnetic field of the head and an outer magnetic field of the head, analyzing the brain magnetic field of the neck and the outer magnetic field of the neck, fusing brain magnetic field information, carrying out noise analysis on the outer magnetic field information, obtaining a reference noise background signal, fusing the brain magnetic field information and subtracting the reference noise background signal, and a magnetoencephalogram with a high signal-noise ratio is obtained. The system and the method have the characteristics of being simple, convenient to implement, high in sensitivity, low in implementation cost, high in reliability, small in space and high in flexibility.