Carbon materials are widely used in various industrial applications due to their outstanding stability and robustness in diverse structures, yet it remains a revolutionary and challenging task in activating low-cost carbon materials for efficient catalysis. Herein, inspired by the successful experimental synthesis, we for the first-time exploited carbon nanotubes (CNTs) encapsulated transition metal (TM) atoms (TM@CNTs) for hydrogen evolution reaction (HER) using density functional theory (DFT) calculations. The Gibbs free energy of the H–C bond on the pristine CNTs is too positive, which prevents the adsorption of H atoms. However, TM@CNTs (TM = Fe, Co, Ni) have superior HER activity than those widely recognized Pt and MoS2 catalysts, benefiting from disrupting the π conjugations and activating the stable sp2 hybridizations among carbon atoms in CNTs. A new set of metal-free catalytic surfaces with strong HER activity have been developed. Meanwhile, the HER activity of graphene nanosheets loaded on the most ubiquitous facet (111) of TMs (TM@G, TM = Fe, Co, Ni) was also calculated. However, TM@G shows inferior HER activity than that of TM@CNTs, which is attributed to the large curvature of CNTs. These new findings manifest a universal strategy for carbon materials activation that will inspire the rational design of carbon-based electrocatalysts for efficient water splitting reaction.