The localization factor is used to describe the band structures for P wave propagating normally in the nanoscaled nearly periodic layered phononic crystals. The localization factor is calculated by the transfer matrix method based on the nonlocal elastic continuum theory. Three kinds of nearly periodic arrangements are concerned, i.e., random disorder, quasi-periodicity and defects. The influences of randomly disordered degree of the sub-layer's thickness and mass density, the arrangement of quasi-periodicity and the location of defect on the band structures and cut-off frequency are analyzed in detail.