Abstract Molybdenum carbide (MoxC) with variable phase structure possesses flexible hydrogen‐binding energy (HBE), which is a promising hydrogen evolution reaction (HER) catalyst. Herein, a hybrid multiphase MoxC freestanding film coupled with Co3Mo (CM/MoxC@NC) is synthesized through the electrospinning method supplemented by the heteroatom incorporation. CM/MoxC@NC surpasses its pure phase counterparts and exhibits remarkable catalytic activity at 114 mV to deliver a current density of 10 mA cm−2 in acid, which is among the first‐rate level performance reported for MoxC‐based catalysts. The subsequent ex situ and in situ characterizations reveal a phase transition mechanism based on self‐catalysis that CoOx depletes the coordinated C of α‐MoC via the interaction, which realizes the assembly of weak HBE α‐MoC and strong HBE β‐Mo2C, and the enhanced utilization of active materials as well. The multiple structures with optimal HBE are in favor of the stepwise reactions of HER, as the study of the correlation between HBE and phase structure revealed. This study discloses the underlying phase transition mechanism and highlights the HBE–structure relationship that should be considered for catalyst design.