By employing first-principles total-energy calculations we studied the electronic and structural properties of the NiSi2/Si(001) and CoSi2/Si(001) interfaces. We found a new structural model that is energetically more stable than previously proposed models and well explains an experimentally observed 2 x I interfacial ordering. The new model is characterized by sevenfold-coordinated interface metals and interface Si dimers, and is achieved by compromising the bonding configuration of the interface metals and the reduction of the number of interface Si dangling bonds. The underlying mechanism of the model is in contrast to that of a semiconductor-surface reconstruction. Finally, the interfacial electronic properties are also presented to give a physical insight into the microscopic mechanism for the Schottky-barrier formation at metal/semiconductor junctions.