Abstract It is highly desirable but still challenging to construct three-dimensional (3D) open porous structure assembled with small-sized and hollow active components for hydrogen evolution reaction (HER). Here, we propose a novel protocol based on electrostatic-repulsion-limited-nucleation strategy and the nanoscale Kirkendall effect to grow FeP nanotube arrays on P-doped graphene. Due to its unique structural features, the resulting electrocatalyst exhibits superior HER activity with an overpotential of 69 mV at the current density of 10 mA cm−2 in 0.5 M H2SO4, comparable to the benchmark Pt/C catalyst. Furthermore, the 3D porous structure shows robust stability toward HER with a negligible current loss after continuous catalysis over 40 h at 10 mA cm−2. The experimental results and density functional theory calculations indicate that the excellent HER activity of the 3D porous structure originates from its increased active sites, reduced transfer resistance and the ideal hydrogen adsorption energy (ΔGH*), as well as better hydrophily upon integration of FeP nanotubes with P-doped graphene. Our protocol provides a new approach to rationally design and fabricate inexpensive 3D open porous structure with high catalytic activity and robust stability for HER.