The invention belongs to the technical field of magnetoencephalography detection, and provides a wearable magnetoencephalography instrument environmental noise suppression system and method. The system comprises a magnetic shielding room, a magnetoencephalography measuring cap, an atomic magnetometer detection sensor array and an atomic magnetometer reference sensor array, wherein a testee wears the magnetoencephalography measuring cap on the head and is placed in the magnetic shielding room, the atomic magnetometer detection sensor array is arranged in the magnetoencephalography measuring cap, and the atomic magnetometer reference sensor array is arranged above the head of the testee. The system is simpler in structure, light and flexible. In addition, according to the wearable magnetoencephalography instrument environmental noise suppression method, gradient arrangement configuration does not need to be carried out on each atomic magnetometer detection sensor, on the basis that the configuration of the detection sensors on the original flexible measuring cap is kept unchanged, the intensity of magnetoencephalography signals can be kept not attenuated, the environmental noise of the shielding room can be effectively suppressed, and the signal-to-noise ratio of the magnetoencephalography signals is improved.