The lithosphere, as the outermost solid layer of our planet, preserves a progressively more fragmentary record of geological events and processes from Earth’s history the further back in time one looks. Thus, the evolution of lithospheric thickness and its cascading impacts in Earth’s tectonic system are presently unknown. Here, we track the lithospheric thickness history using machine learning based on global lithogeochemical data of basalt. Our results demonstrate that four marked lithospheric thinning events occurred during the Paleoarchean, early Paleoproterozoic, Neoproterozoic, and Phanerozoic with intermediate thickening scenarios. These events respectively correspond to supercontinent/supercraton breakup and assembly periods. Causality investigation further indicates that crustal metamorphic and deformation styles are the feedback of lithospheric thickness. Cross-correlation between lithospheric thickness and metamorphic thermal gradients records the transition from intraoceanic subduction systems to continental margin and intraoceanic in the Paleoarchean and Mesoarchean and a progressive emergence of large thick continents that allow supercontinent growth, which promoted assembly of the first supercontinent during the Neoarchean.