Ternary NiSi2−xAlx layer with uniform and smooth NiSi2−xAlx/Si interface has been achieved by Al interlayer mediated epitaxy. A 3 nm Al interlayer is introduced to the Nickel silicidation on Si(001) substrate. The morphology, composition, and micro-structure of the Ni silicide layers are analyzed for different annealing temperatures. It is found that under the assistance of Al atoms, the best quality Ni silicide layer is achieved by annealing at 700 °C. The reduced Ni diffusion and the modified energetics are conducive for the uniform reaction between Ni and Si, resulting in epitaxial ternary NiSi2−xAlx layer on Si(001) substrate.