The natural gas hydrates (NGHs) in the South China Sea are found in unconsolidated clayey-silty sediments, featured by very weak mechanical strength and low permeability. During gas extraction from such unstable, low permeability reservoirs, hydrate dissociation can result in distinct changes in pore properties and flow capability. Thus, it is extremely important to investigate the pore characteristics and gas flow mechanisms in such reservoirs. In this study, five sediment samples including two from the hydrate bearing layer (HBL) and three from the underlying layer (ULL), were taken from an exploration well in the Shenhu area, South China Sea. The pore morphology, pore specific surface area (SSA), total pore volume, porosity, and pore size distribution of these samples have been analyzed to compare the reservoir physical properties of the HBL (after the hydrate has dissociated and disappeared) with the ULL. Results from scanning electron microscopy reveal that the HBL samples without the hydrate present feature larger grain sizes, larger pore apertures and better connectivity than ULL samples. Results of NMR analysis and low temperature N2/CO2-adsorption show that both HBL and ULL samples have high total porosities (42.4%–48.8%) and high SSA (21.17–30.09 m2/g), while the results from centrifugal experiments demonstrate that the producible porosity (defined as the pore volume available for hydrocarbon emplacement) of the HBL samples is about twice (26.6%–30.3%) that of the ULL samples (15.5%–19.6%). The pores in the two sample types are dominated by intra-particle pores of 80 nm, and inter-particle and inter-aggregate pores of 0.2–3 μm. The above differences between HBL and ULL can be used to analyze the pore structure changes occurring as a result of the dissociation of NGHs in the HBL. We assume that on the one hand, formation of NGHs reduces pore pressure, thus resulting in higher effective stress, then compacts the pore space and reduces the total porosity. On the other hand, the release of high-pressure gas during hydrate dissociation could increase the pore aperture and improve pore connectivity, and thus increase the producible porosity of the HBL reservoir. It is also assumed that the flow capacity in the methane production zone in the HBL can be improved by the NGHs dissociation, suggesting that not only the hydrate saturation but also the pore structure changes should be considered when estimating the permeability during the gas production process.