<p>The issue of hydrogen embrittlement within pipeline hydrogen transportation presents a significant impediment to long-distance hydrogen transport. Conventional single-scale research methodologies often fall short in thoroughly elucidating the mechanism underlying hydrogen embrittlement. This paper introduces an innovative multi-scale numerical approach designed to address this issue in alloys, employing molecular dynamics (MD) to model the atomic configuration and assess hydrogen diffusion behavior at the microscopic scale, and utilizing finite element methods (FEM) at the macroscale for loading and solutions. The atom-to-continuum (AtC) multi-scale method serves as an intermediary between them. The accuracy of this multi-scale method is confirmed by comparing the stress–strain curves of alloys with disparate nickel contents (FeNi_1.0, FeNi_0.5, and pure Fe), derived from AtC and MD simulations. This comparison was further supported by quantitative analyses of the evolution of crack tip dislocation density and the hydrogen concentration gradient near the crack tip across the different alloy systems. Under MD simulations, we observed that the dislocation density, interactions, and ultimately, the strength of the alloy, augments concomitantly with an increase in Ni concentration up to an optimal level of approximately 1.0%, beyond which further Ni addition leads to a rebound in hydrogen diffusivity and a decline in mechanical performance. Subsequently, through integration of the AtC multi-scale method with FEM simulations, the mechanical response of cracks under both macro- and micro-calculations is observed. This investigation unveils the fracture mechanism of the long-distance hydrogen transport pipeline steel Fe–Ni alloy and introduces a multi-scale methodology capable of executing large-scale computations, thereby offering a novel tool for material design and applied research.</p>