The adsorption of CH 3 NH 2 on Si(001)-2x1 is investigated using density functional theory slab calculations. When the CH 3 NH 2 coverage is greater than 0.5 ML, we find that the adsorption energetics alter significantly due to a combination of: (i) adsorbate-adsorbate repulsive interactions, (ii) adsorbate-induced electronic structure changes of neighboring dimers, and (iii) hydrogen-bonding interactions. Our calculations show that, among them, adsorbate-adsorbate repulsion plays a major role in determining the two-dimensional ordering of CH 3 NH 2 adsorption at the full coverage of 1.0 ML, leading the zigzag structure to be energetically more favorable than the aligned structure along the dimer row.