Metal-based catalysts ranging from nanoparticles (NPs) to the atomic level usually exhibit varying catalytic performance. The underlying size effect is both fascinating and evident. This study thoroughly investigates the size-dependent effects of Fe-based catalysts on catalytic transfer hydrogenation (CTH) of furfural (FF) at the atomic level. Fe was precisely loaded onto N-doped porous carbon in three forms: single atoms (Fe-SAs/NC), atomic clusters (Fe-ACs/NC), and nanoparticles (Fe-NPs/NC). This was achieved through meticulous control of the iron precursor composition. Remarkably, Fe-SAs/NC exhibited exceptional catalytic efficiency, achieving an FF conversion of 91.3% and a turnover frequency (TOF) of 262.3 h-1 at 110 °C, which is 9.2 times higher than Fe-ACs/NC and an impressive 93.7 times higher than Fe-NPs/NC. The high selectivity of Fe-SAs/NC toward furfuryl alcohol was further substantiated by theoretical calculations. These calculations indicated the benefits from the η1(O)-aldehyde adsorption configuration, formed by the vertical adsorption of FF molecules on the Fe-N4 active sites. Geometrical optimization of the catalyst at the atomic scale enhances its intrinsic catalytic activity and selectivity. The proposed size effect on catalytic activity provides deeper insights into the mechanism of single-atom catalytic hydrogenation and contributes to the exploration of high-performance catalysts at the atomic level.