We report an effect of contact materials (Ag, Au, and Pt) on transport properties of molecular junctions (MJs) based on self-assembled monolayers of 11-(Ferrocenyl) undecanethiol (HSC 11 Fc). Particularly, we observed that the Fc unit directly contacting the Ag-coated atomic force microscopy (AFM) tip in symmetrical MJs, Ag/SC 11 Fc/Ag, leads to a large rectification (∼150) with a giant electrical current density (∼4 × 10 4 A•cm −2 ) at a relatively small negative voltage, −1.5 V. We also observed that the material of the bottom electrode strongly affects the rectified current density but not the rectification ratio in metal/SC 11 Fc/Ag. Optimizing the material of the bottom electrode, especially the energy offset barrier ε o , can produce a large rectification (∼170) at 1.5 V with a giant electrical current, 2.4 × 10 5 A•cm −2 , in asymmetrical MJs using the Ag-coated AFM tip. A simplified Landauer allows us to approximately quantify the electronic coupling strength in symmetrical MJs, Γ Fc-Ag ∼ 5.2 meV, that is 50 times greater than Γ Ag-Fc . In contrast, the electronic coupling strength at the Fc-Au (or Pt) interface is strong (Γ Fc-Au ∼ 120 meV), which leads to a small rectification and high conductance. The direction of the small rectification in the strong coupling regime (Γ Fc-Au/Pt ) can be reversed by controlling the work function of the metal contacts. Overall, our results provide a clear picture of the influence of both the electronic coupling strength and the energy offset barrier on the transport properties and further prove that the conductive-probe atomic force microscopy is a useful, versatile tool for determining structure-transport relationships in molecular junctions.