Hypophosphorous acid (H3PO2) is an important chemical product with wide applications in pharmaceuticals and electroless plating. In this study, bipolar membrane electrodialysis (BMED) was used to produce H3PO2 from sodium hypophosphite salt (NaH2PO2) to replace the traditional preparation methods. The BMED process was optimized in terms of current density, NaH2PO2 salt concentration, and initial NaOH concentration of the base solution. The results indicated that low Na+ leakage occurred at lower salt concentrations. Under the optimum conditions, such a BMED system obtained a high concentration of H3PO2, a low Na+ content, and a low energy consumption, equaling to 1.03 mol/L, 670 ppm, and 1.18 kW h/kg, respectively. To minimize the amount of phosphorous acid (H3PO3) generated from H3PO2 oxidation during the BMED process, a nitrogen aeration operation was applied in both the acid and salt chambers, decreasing the HPO32- content to 251 ppm, which was 44.1% lower than that without a dissolved oxygen content control strategy. The newly produced H3PO3 during the BMED process was reduced by 96.5%. The obtained results indicated that the BMED process has great potential for application in the production of high-quality H3PO2 from NaH2PO2 in industry.