We report on how the local structure and the diffusional motion change upon increasing the alkyl chain length in 1-alkyl-3-methylimidazolium cation ionic liquids. This study has been performed by combining pulse field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy and small angle X-ray scattering (SAXS) experiments. The cationic side chain length varies from ethyl (n = 2) to hexadodecyl (n = 16), while the anion is always bis(trifluoromethanesulfonyl)imide (TFSI). We find that the self-diffusivity of the individual ionic species is correlated to the local structure in the corresponding ionic liquid, namely the nano-segregation into polar and non-polar domains. In agreement with previous results, we observe that for relatively short alkyl chains the cations diffuse faster than the anions; however we also note that this difference becomes less evident for longer alkyl chains and a cross-over is identified at n ≈ 8 with the anions diffusing faster than the cations. Our results indicate that this controversial behavior can be rationalized in terms of different types of cation–cation and anion–anion orderings, as revealed by a detailed analysis of the correlation lengths and their dispersion curves obtained from SAXS data. We also discuss the validity of the Stokes–Einstein relation for these ionic liquids and the evolution of the extrapolated cationic radius that was found to depend non-strictly linearly on n, in agreement with the cation–cation correlation lengths.