The characteristics of the hydrate-bearing layer are important parameters for gas hydrate exploration and exploitation, which can be provided by laboratory analysis. We have carried out a systematic analysis of modern instruments, including the laser grain size analyzer, X-ray computed tomography, scanning electron microscopy, X-ray diffraction (XRD), Raman spectroscopy, gas chromatography, and isotope mass spectrometry, on the hydrate-bearing sediment samples recovered from the Shenhu area in the South China Sea in 2016. We focused on the structure, hydration number, and gas composition of the gas hydrate samples. We also evaluated the effects of sediments on the occurrence and distribution of gas hydrate. Our results showed that the sediments are much finer than those recovered from the Shenhu area in 2007. Some samples are found to contain calcareous microfossils and foraminifera, which are beneficial for dispersed gas hydrate formation. Whereas the only visible hydrate sample (FC4) has not found any bioclast in the sediments. Based on the Raman data and the XRD analysis, the gas hydrates demonstrate typical structure I (sI) hydrates, with cage occupancies of methane molecules higher than 99.3% in large cages and 81.5%–91.4% in small cages, respectively. The crystal lattice parameter is 11.89 Å with the hydration number being approximately 6.0. Methane is obviously the dominant component, ranging from 97.6% to 99.95% in these samples. Comprehensive study of carbon and hydrogen isotopes suggests that the hydrate-bound gases are from biogenic and thermogenic gases in the study area.