The first offshore gas hydrate production test was conducted within the gas-hydrate-concentrated zone (reservoir) of the eastern Nankai Trough, which is considered to be a stratigraphic accumulation. However, the accumulation mechanism for this concentrated zone was not yet well understood. We used core and geophysical log data sets to determine the subsurface geologic architecture and stratigraphic evolution most likely responsible for the stratigraphic accumulation of gas hydrate in the eastern Nankai Trough. Seven depositional sequences were identified based on grain size, bed thickness, sedimentary structure, and stacking patterns. The sequence boundaries were also identified by terminations of seismic reflection. These sequences were attributed to a fourth to fifth-order eustatic sea-level changes because the stacking pattern cycle was in phase with global oxygen isotope curves; the cycle was also identified in the onshore formation during the same period. The reservoir was interpreted as falling-stage systems tract (FSST) and lowstand systems tract (LST). FSST and LST consisted mostly of trough-fill channel deposits. The deposits were represented by alternations of very fine- to fine-grained sand and silt. The reservoir is located in association with the structural wing of the Daini-Atsumi Knoll. The uplift of the knoll was strongly controlled by tectonic events associated with subduction of the pacific plate during Pleistocene time. The muddy deposits above the reservoir were interpreted as condensed section. We identified channel facies pinched out against structural highs, and together, these result in stratigraphic traps. Consequentially, the gas hydrate trapping system was constrained by sedimentary facies, systems tracts, and geographic and tectonic setting. Concepts and data generated in this study can be used for gas hydrate petroleum system analysis such as basin simulation.