Depositional sequences in inland basins are regulated by environmental changes, such as climate change, sediment supply, water input/output, and tectonics. Their mechanisms and driving factors are diverse in each geological setting. This study provides a short-term (millennial to ten thousand years timescales) overview of the sedimentologic evolution in an inland basin located at a high altitude and characterized by fast sedimentation rates (Suwa Basin, central Japan). We employed a multi-disciplinary approach combining sedimentology, paleopedology, and high-resolution sequence stratigraphic analysis of the upper Pleistocene and Holocene succession to clarify the driving factors of the basin's sedimentologic evolution. The depositional systems and systems tracts were divided into meandering fluvial (lowstand systems tract; 26.7–16.5 cal kyr BP), pond/marsh (early transgressive systems tract; 16.5–13.9 cal kyr BP), lacustrine (transgressive systems tract; 13.9–5.8 cal kyr BP), and delta systems (highstand systems tract; 5.8 cal kyr BP–). The boundary between the meandering fluvial and pond/marsh systems corresponds to a transgressive surface appearing as a rising in the lake level (ca. 16.5 cal kyr BP). The boundary between the lacustrine and delta systems corresponds to a maximum flooding surface of the lake (ca. 5.8 cal kyr BP). The lake transgression occurs simultaneously with a decrease in the sediment supply, as suggested by a decrease in the sedimentation rate, the dense development of paleosols, and high TOC and TN showing a lower decomposition rate. The timing coincides with the intensification of chemical weathering, plant succession, and the ascending alpine tree line in the source region during the Northern Hemisphere deglaciation. The depositional sequence in the interior basin might have been easily controlled by changes in the sediment supply due to vegetation/soil cover successions during the glacial-interglacial cycle. Our findings imply that low-frequency depositional sequences observed in such inland basins in the East Asian coastal region may have also been forced by global ice volume changes.