Gas permeability is a key physical parameter to determine the exploitation efficiency of natural gas hydrate (NGH). However, the relevant research mainly focuses on the permeability of homogeneous hydrate reservoirs, there have been no studies of non-homogeneous hydrate reservoirs. Therefore, a novel permeability measurement apparatus was designed in this study, which used two core holders in parallel to achieve the spatio-temporal continuous measurements of gas permeability for non-homogeneous reservoirs. Marine soils obtained from the South China Sea were used to remold the non-homogeneous hydrate reservoirs, including two homogeneous hydrate reservoirs with water saturation of 40% (reservoir A) and 80% (reservoir B), respectively. The constant gas flow of 0.5 ml/s and constant back pressure of 3 MPa was carried out to measure the gas permeability. The experimental results showed that the gas permeability measured in this work had similar regularities with other literature data. When the effective pressure increased from 1 MPa to 6 MPa, the permeability of reservoir A, reservoir B, and non-homogeneous hydrate reservoir decreased from 15.2 mD to 10.9 mD, 10.5 mD to 4.6 mD, and 12.5 mD to 8.5 mD, respectively. In addition, the variation in the non-homogeneous coefficient showed three stages: 1–2 MPa stage, 2–3 MPa stage, and 3–6 MPa stage. What's more, the permeability damage rate of non-homogeneous reservoirs increased by nearly 35% with the increase of effective pressure. These findings obtained by this apparatus will enhance the understanding of gas permeability in the non-homogeneous hydrate reservoirs, and guide further field exploitation of hydrate reservoirs.