The formation of scales in a recirculating water system is a common problem in industrial water treatment; it seriously affects the production in various industries and pollutes the environment. Although conventional scale inhibition methods are effective, they are expensive and harm the environment. Herein, an advanced method is proposed to solve the scaling issue in recirculating cooling water systems using the superconducting high-gradient magnetic field (S-HGMF) treatment. The scale inhibition performance could be improved by changing the magnetic flux density, operation time, and flow rate. The results showed that S-HGMF could increase the number of hydrogen bonds in the recirculating cooling water, enhance molecular interaction, increase the thickness of the ion hydration shell, reduce the nucleation rate, stabilize the water quality, improve the solubility of scale-forming ions, and inhibit scale formation. The scale inhibition performance reached 8.10%. Interestingly, S-HGMF had a memory effect in that it could maintain the scale inhibition effect for some period after treatment completion. Moreover, S-HGMF changed the crystal structure of the scale and promoted the transformation of the scale to a metastable phase. Ultimately, calcite was transformed to aragonite to reduce the precipitation of hard scale (calcite), achieving the purpose of scale inhibition. As a physical method, the application of S-HGMF to inhibit scaling has great potential for industrial applications.