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Cement-based solidification/stabilization (S/S) is an effective technique for remediating heavy metal-contaminated soils, yet its practical application in farmland is constrained by the high cement dosage commonly required and the limited chemical stabilization capacity of conventional systems. In this study, highly dispersible graphene quantum dots (GQDs) are introduced as multifunctional additives to enhance the S/S performance of ordinary Portland cement toward Pb- and Cd-contaminated soils at a cement dosage of 15 wt%. The incorporation of GQDs markedly improves heavy metal immobilization, and the optimum dosage of 0.4 wt% reduces the leaching concentrations of Pb and Cd by 81.7% and 84.4%, respectively, compared with the control sample. Meanwhile, Tessier fractionation shows that GQDs promote the transformation of both metals from labile fractions to more stable forms, with the residual fractions of Pb and Cd increasing from 37.53% to 42.74% and from 49.87% to 56.39%, respectively. Multi-scale characterization further reveals the underlying enhancement mechanism. XRD, FTIR, TG/DTG, and SEM analyses demonstrate that GQDs accelerate cement hydration, promote the formation of C–S–H gel, and refine the microstructure, thereby generating a denser solidified matrix that strengthens physical encapsulation. In parallel, aqueous removal experiments provide supporting evidence for the direct interaction between GQDs and heavy metal ions, while molecular dynamics simulations further reveal GQD-metal interfacial interactions at the atomic scale. These results demonstrate that GQDs enhance heavy metal immobilization through the synergistic effects of hydration promotion and surface chemical interaction, offering an effective strategy for developing high-efficiency low-cement S/S systems for contaminated farmland soil remediation.