To investigate the effect of hydrogen atoms on the size of the plastic deformation zone, molecular dynamics (MD) simulations were performed on a single crack model. The model uses pre-charged hydrogen to quantify the compression effect of hydrogen atoms on the plastic zone during cyclic loading. The results show that stress release at the crack tip occurs mainly in the form of plastic deformation, and the degree of compression in the plastic zone increases with increasing hydrogen concentration. A compression factor, which considers hydrogen concentration, is found with the help of the simulation results. A modified fatigue crack growth rate (FCGR) model, combined with the compression factor, was then used to predict the hydrogen-assisted fatigue crack growth rate. The proposed model shows excellent agreement with the experimental data for X100 steel, and it provides a new framework to describe hydrogen-assisted cracking.