Exploring the relationship between farmland operational scale and farmland ecological efficiency can provide a scientific basis for agricultural modernization and sustainable use of farmland in Huang-Huai-Hai plain. Based on a panel data of cities at prefecture level and above in Huang-Huai-Hai plain from 2007 to 2020, this study evaluated the ecological efficiency of farmland operation by the super-efficiency SBM-Undesirable model and analyzed the impact mechanism of farmland operational scale on the ecological efficiency of farmland by the Tobit model, the threshold model and the mediating effect model. Result shows that: 1) The overall ecological efficiency of farmland in the study area is declining, with uneven spatial development and widening regional differences, presenting a phenomenon of “high-high aggregation and low-low aggregation”; 2) There is a “U-shaped” relationship between the expansion of farmland operational scale and farmland ecological efficiency, and there is a single threshold effect, with a threshold value of 0.38 hm2/person. When the farmland scale is lower than the threshold value, the expansion of farmland operational scale will reduce farmland ecological efficiency, and vice versa, it will improve farmland ecological efficiency; and 3) The input intensity of chemical fertilizer, pesticides and machinery plays an mediating role in the impacts of farmland operational scale on the farmland ecological efficiency. Based on the above results, to promote the improvement of ecological efficiency of farmland and realize the sustainable use of regional farmland, this paper suggests: strengthening the policy support of farmland scale management, promoting farmland operational scale to cross the threshold, building a green agricultural production and management system, and promoting the transformation of agriculture to green development.