Interaction between the undercoordinated atoms at sites surrounding defects, at edges, or at surfaces has been recognized as the key to the unusual behavior of low-dimensional systems. However, determination of the binding energy of an isolated atom and its bulk shifts with a clear insight into the origin of the size effect has been a longstanding challenge. Here we show that a combination of the X-ray photoelectron spectroscopy and Auger electron spectroscopy, or Auger photoelectron coincidence spectroscopy (APECS), the band theory, and the recently developed bond order-length-strength (BOLS) correlation mechanism [Sun. Prog. Solid State Chem. 2007, 35, 1] has enabled us to gain quantitative information regarding the L(2p(3/2)) and M(3d(5/2)) energy levels of an isolated Ni atom and their bulk shifts by numerically analyzing the size dependence of these energy bands of Ni nanostructures. Meanwhile, the correlation between the Auger kinetic energy, E-K, and the APECS-involved L and M lines has been first established, clarifying that the energy shift of the Auger parameter, or the sum of the absolute energy shift of the E-K and E-L, is twice that of the M level, Em. Findings affirmed that the size-induced core-level shifts of nanostructures originate from the broken-bond-induced local strain and the associated skin-depth quantum trapping, which results in deeply- and densely trapped charge and energy in the surface skin of two interatomic spacings in depth.