Atomic catalysts (ACs) have been considered as promising catalysts for efficient hydrogen production through water splitting. Herein, we report an AC with single Mn atoms highly dispersed on the surface of graphdiyne–coated copper hydroxide nanowire arrays (Mn–GDY/Cu(OH)x NWs). By anchoring of Mn atoms on GDY, the specific surface area, the number of active sites, and the stability of the catalyst are greatly improved. Detailed characterizations reveal that the high hydrogen and oxygen evolution reaction (HER/OER) catalytic activity of the catalyst is induced by the strong incomplete charge transfer effect between the metal atoms and the GDY. These advantages enable the electrocatalysts can drive a current density of 10 mA cm−2 at low overpotentials of 188 mV and 130 mV for OER and HER, respectively, together with excellent long–term stability. Remarkably, the alkaline electrolyzer using Mn–GDY/Cu(OH)x as both cathode and anode electrodes can reach 10 mA cm−2 only at a much low cell voltage of 1.50 V.