Earthquakes and tsunami repeatedly occur in the coastal areas of the Japanese islands, which are located on the margin of continental plates. Paleotsunami deposits in these areas provide important clues regarding the reconstruction of past marine incursions by earthquakes and tsunami. The Miyazaki plain on the Pacific coast of southwest Japan along the Nankai–Suruga trough has been also affected by marine incursions by previous interplate earthquakes and tsunami. Tsunami deposits are usually identified by their geological, sedimentological, and geochemical characteristics. In the present work, portable energy dispersive X-ray fluorescence spectrometry (portable XRF), X-ray analytical microscopy (XGT), statistical analyses, and heavy mineral analyses were performed to characterize the paleotsunami deposits of the Kanbun Hyuganada earthquake (age, 1662 common era) in the SY03 core from the south Miyazaki plain. Our new findings can be summarized as follows: (1) Increases in the Ti-normalized values of S, Ca, Fe, and Sr, and depletions of K were observed in the deposits; (2) Accumulation of Zr and heavy minerals such as zircon, likely related with the high-energy tsunami, were found in the deposits; (3) Cluster analyses of the geochemical data acquired from the SY03 core by the portable XRF distinguished the paleotsunami deposits on the south Miyazaki plain. Furthermore, we also compiled the geochemical data of samples from the Shizuoka (central Japan), Sendai (Pacific coast of northeast Japan), and Miyazaki plains. Increases in Ti-normalized values (e.g., Sr/Ti) were found in these paleotsunami deposits. Our studies indicate that geochemical approaches are suitable for the characterization and exploration of paleotsunami deposits on the several coastal areas of Japan.