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• Saccharomycetes are used as green phosphorus source to produce metal phosphides. • Interface phosphating for solid-solid contact can efficiently utilize phosphorus. • Graphitizing & migration of metal-catalyzed carbon matrix to form hollow structure. • The Ni/Ni 3 P heterostructure can weaken strong Ni–H bonding to obtain small Δ G H*. • Achieve hydrogen production from wastewater treatment at low input voltages. The development of new, clean and efficient catalytic materials for hydrogen evolution reaction (HER) has become extremely unstoppable. Herein, the heterostructural Ni-Ni 3 P nanoparticles embedded into N\P co-doped carbon shells on 3D graphene frameworks (Ni-Ni 3 P@NPC/rGO) was synthesized via an in situ phosphatization of nickel well-integrated with the structure engineering of carbon matrix derived from saccharomycetes. The in-situ phosphating process of nickel using P source provided by saccharomycetes is particularly simple, economical and environmentally friendly. In addition, the as-prepared Ni-Ni 3 P@NPC/rGO exhibits superior bifunctional electrocatalytic performance toward both HER (extremely low overpotential of 113 mV at 20 mA cm–2) and urea degradation reaction (UDR, only 1.38 V to attain 50 mA cm–2). Furthermore, a two-electrode electrolyzer employing the 3D block electrode (Ni-Ni 3 P@NPC/rGO/GFB) couple on both cathode and anode, can produce higher current density with lower voltage in urea-based wastewater splitting less than pure water splitting (saved 448 mV to deliver 500 mA g–1). [ABSTRACT FROM AUTHOR]