Hydrogenation of nitriles represents as an atom-economic route to synthesize amines, crucial building blocks in fine chemicals. However, high redox potentials of nitriles render this approach to produce a mixture of amines, imines and low-value hydrogenolysis byproducts in general. Here we show that quasi atomic-dispersion of Pd within the outermost layer of Ni nanoparticles to form a Pd1Ni single-atom surface alloy structure maximizes the Pd utilization and breaks the strong metal-selectivity relations in benzonitrile hydrogenation, by prompting the yield of dibenzylamine drastically from ∼5 to 97% under mild conditions (80 °C; 0.6 MPa), and boosting an activity to about eight and four times higher than Pd and Pt standard catalysts, respectively. More importantly, the undesired carcinogenic toluene by-product is completely prohibited, rendering its practical applications, especially in pharmaceutical industry. Such strategy can be extended to a broad scope of nitriles with high yields of secondary amines under mild conditions.