•A facile organic–inorganic hybrid method was proposed to fabricate the bimetallic phosphide of MoP-RuPx/NPC.•The bimetallic phosphide catalyst with MoP-RuPx was encapsulated into porous N, P co-doped carbon nanosphere.•The improved HER activity of MoP-RuPx/NPC comes from porous nanostructure, abundant defects and the synergistic effect of bimetallic phosphide. Hydrogen evolution reaction (HER) serves as a crucial half reaction in electrolytic water splitting. Pt is deemed to the most active HER electrocatalyst, but the scarcity and high cost of Pt limit its massive application. Developing efficient, low-cost and well-structured HER catalysts is quite vital for advancing the development of water electrolysis technology. Herein, we present a facile organic–inorganic hybrid method to achieve a novel bimetallic phosphide of MoP-RuPx/NPC catalyst, showing superior electrocatalytic activity with an overpotential of 24 and 94 mV at 10 mA cm−2 in alkaline and acid media, respectively. Moreover, MoP-RuPx/NPC also exhibits an outstanding electrochemical stability with a negligible degradation in HER activity after long-term stability measurements. The eminent electrocatalytic performance of MoP-RuPx/NPC catalyst should be ascribed to the high surface specific area, multiple heterogeneous interfaces, strong electronic synergistic effect between MoP and RuPx, and abundant defects. The organic–inorganic hybrid strategy implemented in this work can be used for synthesizing other bimetallic phosphide catalysts.