Hydrogen embrittlement is a well-known and fatal degradation phenomenon in metals and alloys for infrastructures and power plants. Since hydrogen embrittlement is especially vulnerable when lattice defect exists in materials, nano-scale observation and simulations are required to diagnose and predict the trajectories of the diffusing hydrogen. Therefore, molecular dynamics simulation is applied with ReaxxFF(reactive force field) to observe the diffusion and concentration of hydrogen molecules in steel and its compound. Ferrite/cementite interface and ferrite structure containing vacancy cluster are constructed for this study. The work of separation of the ferrite-cementite interface is determined from a model I decohesion test. In addition, the critical temperature at which hydrogen atoms actively start to aggregate into pores inside the ferrite structure is determined.