Chronologically well-constrained loess-palaeosols (recorded glacial and inter-glacial climate) revealed pedogenesis induced ionic substitutions, caused end-member compositional deviations in illite and chlorite, linked to widespread climatic changes occurred during Late Pleistocene. Further, micro-level climatic resolution is yet to be resolved. Thus, layer-wise X-ray diffraction analyses of clay separates, followed by Rietveld refinement revealed varied cell parameters and interatomic distances. Obtained values for detrital and pedogenic illite and chlorite when plotted against stratigraphic succession show notable changes in the crystallographic axes. The illite lattices associated with inadequately pedogenized palaeosols have been altered into illite/smectite mixed layers, but, the chlorite lattices represent expansion of a-, b- and contraction of c-axes with much greater amount of distortions, suggestive of warm-humid and acidic environment. The detrital 48, 44 and 83, 74 bonded illite and chlorite with 2 sub-types each, when pedogenized retained 48, 44 and 34; and 83 and 74 bonds (in their neo-formed 3 and 2 sub-types), respectively. The Al–O bond shows expansion, but, unchanged Si–O and decreased Si–K and K–O bonds show loss of Al and retention of Si and K ions in the illite lattices. The illite with 32 atoms and 48 bonds represent contraction of K–O, Si–K, Al–O and Si–O bonds caused bond reinforcement; however, loss of Al3+ reflects all-out illite alteration. Owing to Al–O and K–O bond expansion, major K+ and Al3+ ionic loss occurred during the LGM, however, further ionic loss depends upon the magnitude of the loess-palaeosol weathering that they have suffered. The climate sensitive Fe, Mg and Al ionic losses for Fe–O, Mg–O and Al11–O9 bond length expansions were recognized in the chlorite lattices. Such ionic losses are common, but, complete distortion is attributed to Al, Si, Fe and Mg ionic losses, followed by weakening of Al–O, Si–O, Fe–O and Mg–O bonds. Though, Si–O4 and Fe1–O4 bonds, and Si and Fe1st ions remain intact.Thus, three major glacial episodes of ~5 ka each occurred under alkaline environment, but, intervened by two successive cycles of 55 ka each, encompassing three alternate warm and cold climatic sub-cycles of 12–15 ka. But, the coldness increases with each warm-cold sub-cycle that attained the glacial maxima. Further, these events correlate well with the deep-sea records of the North Atlantic (MIS-1 to MIS-5e) and CLP loess-palaeosols (~127 ka).