Bottom-simulating reflections (BSRs) in seismic data have been widely accepted to indicate the base of the methane gas hydrate stability zone (MGHSZ), and free gas was thought to exist only below it. However, real geologic systems are far more complex. We have evaluated the results of 3D seismic, logging while drilling, in situ, and coring measurements at a venting gas hydrate system in the Shenhu area of the South China Sea. Our studies reveal that free gas has migrated upward through the thermogenic gas hydrate stability zone into the MGHSZ and become a part of the gas hydrate system. Seismic amplitude anomalies and core results suggest the presence of free gas above the base of MGHSZ at 165 mbsf and the presence of thermogenic gas hydrates below it in well SC-W01. Analyses of P-wave velocity, S-wave velocity, density, and porosity logs reveal that free gas occurs above and below the MGHSZ as well. Integrating log and core analysis with seismic interpretation suggests that the variation in seismic amplitude within the chaotic zone is associated with variable gas saturations, and a large amount of methane and thermogenic gases accumulate near the complex BSRs. We suggest that relative permeability likely plays a significant role in the free-gas distribution and the formation of gas hydrates within a venting gas hydrate system, whereas the effect of dissolved gas short migration is not ignored. Our results have important implications for understanding the accumulation and distribution of gas hydrates and free gas in the venting gas hydrate system and seeps at the seafloor.