Abstract Natural gas hydrates were widely distributed in marine sediments and permafrost areas, which have attracted global attentions as potential energy resources. Permeability characteristics of sediments determine the technical and economic feasibility of natural gas energy production and energy production efficiency from the hydrate reservoirs. But clay possesses significant water sensitivity and swelling characteristics in hydrate reservoirs, which may significantly affect permeability changes. Therefore, the mechanism significantly affects the gas energy production of hydrate reservoir. This study presented here focuses on the phenomenon of gas phase permeability changes due to hydrate decomposition. In this paper, the experimental study of the methane hydrate decomposition was carried out by depressurization, and the gas phase permeability characteristics changes of three kinds of clay before and after hydrate decomposition were investigated. The results show that the gas phase permeability of clay decreases gradually with the hydrate decomposition. The possible explanations for this phenomenon are that the formation of the bound water and swelling of clay, which block the pore channel of gas flow. In addition, after the hydrate complete decomposition, the value of the gas phase permeability damage (Ratio of permeability after hydrate decomposition to that before hydrate decomposition) of the clay firstly decreases and then increases with the increase of initial hydrate saturation. When hydrate saturation is 20%, Hydrate decomposition has the most influence on gas phase permeability damage of clay. And after the hydrate decomposition, the swelling of kaolin is less than illite and the swelling of illite is less than montmorillonite. The predicted porosity of clay after hydrate decomposition is calculated by Ives and Pienvichitr model and Tien’s model. This work could be valuable to research on the gas energy production from the hydrate reservoir.