Utilizing plant extracts for soil washing is a promising and cost-efficient strategy to permanently remove toxic metals from farmland soils. However, the efficiency of current plant extracts in heavy metals removal is constrained by the need of excessively high liquid-solid ratios (>10:1), which limits their practical application in the farmland soils. To address this challenge, we developed a novel binary washing agent consisting of Fructus mume residue extract (RPM) and methylglycinediacetate acid (MGDA). Through optimization experiments, we determined an optimal composition of 50 g L−1 RPM and 0.34 g L−1 MGDA (RPMG3), which exhibited a remarkable synergistic effect on the removal of Cd and Cu from two polluted farmland soils. Compared to the single use of RPM or MGDA, RPMG3 increased metal removal efficiency by 44.6%–303.8% in the alkaline dryland soil and 55.8%–141.9% in the slightly acidic paddy soil, at an optimum liquid-solid ratio of 2:1. The contents of soil Cd and Cu can be reduced to below the risk screening values via acid activation, metal ion exchange, and complexation of functional groups. Moreover, the potential ecological risks associated with Cd in the soils were significantly mitigated due to the decrease in exchangeable and reducible Cd fractions following RPMG3 washing. Additionally, RPM and RPMG3 washing led to enhancements in soil organic carbon and nutrient concentrations, as well as increased activities of soil enzymes including catalase, urease, and β-glucosidase. Notably, RPMG3 washing exhibited the most pronounced promotion effect on wheat seed germination and growth. Taken together, the binary complex of RPMG3 demonstrates potential as an environmentally friendly green washing agent capable of in reducing heavy metals from farmland soil with great efficiency, even at low liquid-solid ratios.