Employing a low-cost and highly efficient electrocatalyst to replace Pt-based catalysts for hydrogen evolution reaction (HER) has attracted increasing interest in renewable energy research. Earth-abundant transition metals such as Fe, Co and Ni have been investigated as promising alternatives in alkaline electrolytes. However, these non-precious-metal catalysts are not stable in acids, excluding their application in the acidic solid polymer electrolyte (SPE). Herein, we report a strategy to encapsulate 3d transition metals Fe, Co and the FeCo alloy into nitrogen-doped carbon nanotubes (CNTs) and investigated their HER activity in acidic electrolyte. The optimized catalysts exhibited long-term durability and high activity with only a textasciitilde70 mV onset overpotential vs. RHE which is quite close to that of commercial 40% Pt/C catalyst, demonstrating the potential for the replacement of Pt-based catalysts. Density function theory (DFT) calculations indicated that the introduction of metal and nitrogen dopants can synergistically optimize the electronic structure of the CNTs and the adsorption free energy of H atom on CNTs, and therefore promote the HER with a Volmer-Heyrovsky mechanism.