<p>Continental crust is the long-term achieves of Earth’s evolution across billions of years. The continental rocks could have been modified by various types of geological processes, such as metamorphism, weathering, and reworking. Therefore, physical or chemical properties of rocks through time record the composite effects of geological, biological, hydrological, and climatological processes. Temporal variations in these time series datasets could provide important clues for understanding the co-evolution of different layers on Earth. However, deciphering Earth’s evolution in deep time is challenged by incompleteness, singularity, and intermittence of geological records associated with extreme geological events, hindering a rigorous assessment of the underlying coupling mechanisms. Here, we applied the recently developed local singularity analysis and wavelet analysis method to deep-time U-Pb age spectra and sedimentary abundance record across the past 3.5 Gyrs. Standard cross-correlation analysis suggests that the singularity records of marine sediment accumulations and magmatism intensity at continental margin are correlated negatively (<i>R</i>² = 0.8), with a delay of ∼100 Myr. Specifically, wavelet coherence analysis suggests a ∼500–800 Myr cycle of correlation between two records, implying a coupling between the major downward processes (subduction and recycling sediments) and upward processes (magmatic events) related to the aggregation and segregation of supercontinents. The results clearly reveal the long-term cyclic feedback mechanism between sediment accumulation and magmatism intensity through aggregation of supercontinents.</p>