Noble metal materials have been identified as high efficiency catalysts for electrocatalytic reduction of nitrate, and the synthesis and manufacture of high catalytic activity and environmentally friendly catalysts of activating hydrogen for water purification applications is extremely attractive. In this work, the Pd–Cu single-atom catalysts (Pd–Cu-N-BC) were first prepared by direct growth of Pd–Cu single-atom on bamboo biochar by regulating the concentration of precursors and doping method, and then enhanced electrocatalytic reduction nitrate performance and N2 generation. The results showed that Pd–Cu-N-BC displayed excellent catalytic activity and reusability in electrocatalytic reduction nitrate with a low potential of 0.47 V vs. RHE (@10 mA cm−2). The maximum nitrate removal efficiency and N2 generation could reach about 100% and 72.32% within 180 min, respectively. The density functional theory (DFT) calculations confirmed that Cu atoms could catalyze the electrochemical reduction of nitrate to nitrite, and Pd atoms anchored in the nitrogen-doped biochar (N-BC) lattice could catalyze electrochemical reduction of nitrite to N2 involving the formation of hydrogen radical (H*). The characterization results of XANES showed that electronic synergistic effect between Pd and Cu single atoms significantly promotes the N2 production through hydrogenation while inhibiting the generation of byproducts, leading to significantly enhanced electrocatalytic reduction of nitrate to N2. Finally, Pd–Cu-N-BC was designed as a 3D particle electrode for enhanced electrocatalytic reduction of nitrate, exhibiting excellent stability and reusability, which could be considered as a suitable candidate for applications in the remediation of nitrate contamination.