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Abstract Layering within the cratonic lithosphere has been explored and reported in different cratons using a range of techniques. However, whether there exists a common feature in the lithosphere for all the cratons is not clear yet. In this study, we carry out a comparison study between the Yilgarn craton in Western Australia and the Superior craton in North America that have never been in direct contact throughout their tectonic history. To have a detailed description of the lithospheric layering in both cratons, we employ receiver function analysis with harmonic decomposition to characterize the anisotropic seismic structure beneath 4 long‐operating sites in each craton. We can identify multiple unique anisotropic boundaries above 170 km at all sites in both cratons. Properties of the anisotropic boundaries are distinct both within and across the cratons. Our observation agrees with a commonly accepted view of the cratonic lithosphere consisting of at least two layers. Moreover, it adds new details to the previous view and reveals lateral variations of the anisotropic properties over distances of a few hundreds of kilometers. Such variations in anisotropic properties likely reflect the tectonic history predating the final assembly of cratons, and suggest horizontal movements are necessary for the formation of cratonic lithosphere.