Sequence stratigraphy analysis is one of the most important tasks in evaluating and characterizing the reservoir system within a basin. However, it is very hard to identify the system tracts and lithofacies using well logs for the conglomerate reservoirs because of the strong lithology heterogeneity. Based on the fact that the system tracts and lithofacies usually illustrate cycle features within the basin, we decompose the well logs into different intrinsic modes to characterize the sequence units and lithofacies at different scale. First, we analyze the log response to lithologies to determine the well logs used for sequence analysis. Then, we use variational mode decomposition to decompose the selected well logs into an ensemble of different band-limited intrinsic mode functions, each with its center wavenumber. Finally, we interpret the sequence stratigraphy and lithofacies using corresponding decomposed modes. We validate the effectiveness of our method in the lithofacies and sequence identification for a conglomerate reservoir in the Shengli oil field, Bohai Bay Basin, east China. The decomposed intrinsic modes with a larger center wavenumber perfectly characterize the sequence units at a larger scale, whereas the decomposed intrinsic modes with a smaller center wavenumber reveal the lithofacies changes at a smaller scale. The application illustrates that it is much more convenient and easier for sequence stratigraphy analysis to integrate the original and decomposed logs.