Reducing kinetic energy barriers and developing accessible active sites are critical to deliver high hydrogen evolution reaction (HER) efficiency. In this paper, we synthesized defect-modulated and heteroatom (boron)-functionalized three-dimensional (3D) bowl-shaped Ti_3−xC₂T_y MXene (B-TCT) nanocavities coupled with the vertical growth of MoSe₂ nanoflakes. The B-TCT@MoSe₂ nanohybrids catalyst delivers the overpotentials of 49.9, 52.7, and 67.8 mV to reach a HER current density of 10 mA·cm⁻² under acidic, alkaline, and neutral conditions, respectively. Such outstanding HER activity is predominantly attributed to the heteroatom functionalization, self-adapting Ti vacancy (V_Ti) defect modulation, and spatial configuration design in the 3D B-TCT nanocavity, which synergistically regulate the electronic structure, activate the basal plane/edge unsaturated sites, and reduce the reaction energy barrier. Experimental and theoretical calculations demonstrate that strong heterogeneous interfacial bonding interactions between B-TCT and MoSe₂ can dramatically reduce the free energy of hydrogen adsorption and facilitate efficient interfacial charge migration, thus essentially improving the HER kinetics. We used this 3D porous nanohybrid system assembled by defect-rich lamellar structures to elucidate the advantageous synergistic effects of multiple mechanisms among defect structure, heteroatom functionalization, and interfacial coupling, which provided important insights for the development of efficient hybrid-type catalysts.