Imaging the heart magnetic field to diagnose is a cutting-edge development direction to overcome cardiovascular diseases. Since the heart's magnetic field is extremely weak, the magnetic field must be detected in a magnetic shielding device when imaging the heart magnetic field. To improve the antidisturbance ability of the magnetic shielding device, this article proposes a disturbance suppression based high-precision magnetic field compensation (MFC) method for a magnetic shielding cylinder (MSC). A set of experimental system based on a MSC is built up and experiments verify the effectiveness of the proposed method in suppressing the external disturbance magnetic field.