Shot peening (SP) is a common surface-strengthening technique for the fatigue resistance improvement of γ/γ′ dual-phase Ni-based superalloys, whereas the coordinated deformation mechanism of γ/γ′ dual-phase architecture and its role in fatigue strengthening remain elusive. In this study, unique graded surface nanostructures were reported for the first time in shot peened single-crystal (SX) superalloys that possessed a six-fold fatigue life improvement compared to their non-treated counterparts. The graded nanostructures were composed of (ⅰ) outermost “fully nanocrystallized zone” (average grain size ∼55 nm) with nearly complete dissolution of γ′ precipitates, (ⅱ) “transition zone” with partially fragmented γ′ precipitates, and (ⅲ) “partially nanocrystallized γ channel zone” with the emergence of nanograins merely in the γ channels. These observations advance the previous understanding that only FNZ was present in the SP-treated γ/γ′ SX superalloys. The graded surface nanostructures together with work hardening and residual stress hindered strain localization and delayed crack initiation in the original soft γ matrix channels, thus prolonging the fatigue life. The collective outcomes of this work not only provide in-depth insights into the deformation mechanisms in shot-peened γ/γ′ dual-phase superalloys but also can be used to further tune their surface nanostructures and hence mechanical properties.