Effect of a permanent magnet field on the scale inhibition property of circulating water was investigated. Orthogonal experiments of L16(45) were performed and analyzed using the range analysis method. The operating parameters included magnetic field intensity, initial concentration of Ca2+ and Mg2+, magnetic treatment time, temperature, and flow velocity. Scale inhibition rate, hardness, relative variation in the proportion of free water molecules, electrical conductivity, and relative variation of molecular energy were chosen as the objectives. In addition, the morphology and the composition of CaCO3 and MgCO3 scale were studied by X-ray diffraction analysis. The optimal conditions were initial concentration of 900 mg/L, magnetic field intensity of 0.5 T, temperature of 303 K, time of 54 h and flow velocity of 0.17 m/s. The nuclear magnetic resonance results demonstrated that the number of hydrogen bonds increased between water molecules and hydrated ions. The magnetic field can promote the increase in the number of hydrogen bonds, which can inhibit the formation of calcium and magnesium carbonate precipitation. Moreover, the ratio of calcite, aragonite and vaterite will be changed at different magnetic field intensities, and the aragonite ratio will reach the peak at the optimum conditions.