The International Ocean Discovery Program (IODP)351 expedition drilled unconsolidated deep-sea sediment sequences in the Amami Sankaku Basin of the Philippine Sea, establishing an accurate age model through magnetostratigraphic methods. This study conducted cyclostratigraphic analysis on the 0–127.58m interval of Site U1438 in the Amami Sankaku Basin, revealing discrepancies between cyclostratigraphic and magnetostratigraphic results. Cyclostratigraphic analysis identified well-preserved Milankovitch cycles in three intervals (0–127.58m, 0–80m, and 0–50.28m). However, the thickness of the 405ka sedimentary cycles in the 0–127.58m interval exhibited significant deviations compared to other intervals. By comparing cyclostratigraphic and magnetostratigraphic ages, it was observed that ages aligned closely above 83m, but diverged progressively below this depth. This suggests unstable deposition rates within the 83–113m interval. Integrating prior research, we propose that tectonic events in the Amami Sankaku Basin and adjacent regions during the 6–12 Ma period significantly influenced deposition rates, leading to pronounced variations in Milankovitch cycle thickness during this interval.