A meshless radial basis function (RBF) collocation method based on the Eringen nonlocal elasticity theory is developed to calculate the band structures of ternary and quaternary nanoscale multi-layered phononic crystals (PNCs) with functionally graded (FG) interlayers. Detailed calculations are performed for anti-plane transverse waves propagating in such PNCs. The influences of FG and homogeneous interlayers, component number, nonlocal interface imperfections and nanoscale size on cut-off frequency and band structures are investigated in detail. Numerical results show that these factors have significant effects on band structures at the macroscopic and microscopic scales.