Interlayer friction stir processing (FSP) has been proved to be an effective method of enhancing the mechanical properties of wire arc-directed energy deposited (WA-DED) samples. However, the original deposition structure was still retained in the FSP-WA-DED component besides the processed zone (PZ), thus forming a composite structure. Considering the material utilization and practical service process of the deposited component, more attention should be paid on this special composite structure, but the relevant investigation has not been carried out. In this study, an Al-Mg-Sc alloy was prepared by WA-DED with interlayer FSP treatment, and the composite structure was firstly investigated. Almost all of the pores were eliminated under the pressure effect from the tool shoulder. The grains were further refined with an average size of about 1.2 μm in the PZ. Though no severe plastic deformation was involved in the retained WA-DED deposition zone, comparable tensile properties with the PZ sample were obtained in the composite structure. Low ultimate tensile strength (UTS) of 289 MPa and elongation of 3.2% were achieved in the WA-DED sample. After interlayer FSP treatment, the UTS and elongation of the PZ samples were significantly increased to 443 MPa and 16.3%, while those in the composite structure remained at relatively high levels of 410 MPa and 13.5%, respectively. Meanwhile, a high fatigue strength of 180 and 130 MPa was obtained in the PZ and composite structure samples, which was clearly higher than that of the WA-DED sample (100 MPa). It is concluded that the defects in traditional WA-DED process can be eliminated in the composite structure after interlayer FSP treatment, resulting in enhanced tensile and fatigue properties, which provides an effective method of improving the mechanical properties of the WA-DED sample.