Electrochemical water splitting is a possible way of realizing sustainable and clean hydrogen production but is challenging, because a highly active and durable electrocatalyst is essential. In this work, we integrated heterogeneous engineering and vacancy defect strategies to design and fabricate a heterostructure electrocatalyst (CoPv-MoxPv/CNT) with abundant phosphorus vacancies attached to carbon nanotubes (CNTs). The vacancy defects enabled the optimization of the electronic structure; thereby, the electron-rich low-valent metal sites enhanced the ability of nonmetallic P to capture proton H. Meanwhile, the heterogeneous interface between bimetallic phosphides and CNTs realized rapid electron transfer. In addition, the Co, Mo, and P active species in the electrocatalytic process exposed increased amounts of active sites featuring porous nanosheet structures, which facilitated the adsorption of reaction intermediates and thus enhanced the hydrogen evolution reaction performance. In particular, the optimized CoPv-MoxPv/CNT catalyst possesses an overpotential of 138 mV at a current density of 10 mA cm-2 and long-term stability for 24 h. This work offers insights and possibilities for the engineering and exploration of transition metal-based electrocatalysts through combining multiple synergistic strategies.