The strong Mo-N bond restrains the catalytic activity of metallic Mo in ammonia synthesis. In this study, the semi-empirical calculations in conjunction with the density functional theory calculations, Brønsted-Evans-Polanyi relationship and microkinetic modeling were used to evaluate the rate of ammonia synthesis on model active sites of Mo-based alloys, nitrides, and clusters with a modified Mo-N bond. It was found that active sites of binary alloys Mo δ Me 1−δ (0 ≤ δ ≤ 1; Me = Co, Pt, Ir, Rh) show the synergetic behavior. The sites of ternary Mo 3 Me 3 N (Me = Mo, Co, Pt, Ir) and Mo 2 N-type nitrides revealed higher activities than sites on Mo planes due to an extra Mo bond with the lattice N atom. The sites of octahedral clusters Mo 3 Me 3 N (Me = Mo, Co, Ir, Pt) exhibited higher catalytic activity than the sites of nitrides because their Me-N bonds are weaker than Mo-N. It was also found that tetragonal Mo 2 Me 2 (Me = Co, Pt, Ir) and bi-tetragonal clusters Mo 3 Me 2 (Me = Co, Ir, Pt) are the best cases because their sites provide the optimal combination of local structure and thermodynamics. Catalytic activities of the most active sites, relative to the Fe-C 7 center, were found to change in the row 18.4 (threefold site Mo 2 Ir 1 in cluster Mo 3 Ir 2 ), 7.3 (Mo 2 in cluster Mo 2 Ir 2 ), 3.9 (Mo 2 Pt 1 in cluster Mo 3 Ir 3 N), 3.8 (M 3 on alloy Mo 0.78 Ir 0.22 ), 2.0 [Mo 3 Pt 1 on the plane (100) of Mo 3 Pt 3 N], 0.57 [Mo 3 on the plane (111) of Mo 2 N], and 0.03 [Mo 4 on the plane Mo(110)-(1 × 2)]. The design of tailor-made catalytic sites suggested in this paper can probably be applied to other catalytic systems.