Stratigraphic layered pore-filling gas hydrates are identified above the bottom simulating reflector (BSR) using the well log and core data acquired at Sites W11 and W17 during the third gas hydrate drilling expedition conducted by China's Geological Survey/Guangzhou Marine Geological Survey (GMGS3) in the South China Sea. A seismic profile near Site W17, reveal the presence of two BSRs (i.e., double BSR), which we show to relate to zones of structure I gas hydrate (I-BSR) and structure II gas hydrate (II-BSR). Well log data from Site W17 between the “I-BSR” (projected depth of 250 mbsf) and “II-BSR” (projected depth of 330 mbsf) showed anomalous responses for gas hydrate-bearing sediments with high resistivity, high S-wave velocity, and alternating high and low P-wave velocities. Pressure core data support the interpretation that structure II gas hydrate occurs at a depth of 263 mbsf at Site W17. The cross-plot between log-derived neutron and density porosities reveals a free gas-bearing layer at a depth of 258–270 mbsf, suggesting gas hydrate coexists with free gas between the “I-BSR” and the “II-BSR.” Synthetic seismograms generated from the P-wave velocity and density logs further support the presence of free gas in this section. Based on the coexistence of hydrate, free gas and water, the simplified three-phase equation (STPE) was modified to simultaneously estimate free gas and hydrate saturations beneath the “I-BSR” from P-wave and S-wave velocity logs, assuming uniform or patchy distributions of free gas. The estimated free gas and hydrate saturations, together with gas compositions from pressure core samples, collectively indicate that structure II gas hydrate and free gas are interbedded and coexist below the “I-BSR” at Site W17. Our study of the coexistence of gas hydrate and free gas between the double BSR at Site W17 provides new insights into gas hydrate systems in nature that contain more complex gas chemistries.