The surface structural characteristics of Fe quantum wires prepared by two electrochemical methods in solution were studied by their conductance changes caused by the interactions between the quantum wires and specific molecules. Once ascorbic acid was added into the solution, the conductance of the Fe junction decreased to a lower value while for the dopamine adsorption, the conductance showed no obvious change. We proposed that there were some iron(II) ions on the surface of atomic-scale Fe junction, not iron(III) ions, and these iron(II) ions played a significant role for the conductance change. This mechanism was further enhanced by the following two experiments. When exposing the quantum wire to sodium borohydride, the conductance increased to a higher value, and the conductance increase was also observed with an electrochemical reduction process, which provided additional evidence for the proposed mechanism.