Understanding the combined effect of stress, pore pressure and temperature on methane permeability is crucial to hazards detection and mitigation in deep coal mining. It is well known that mine temperature increases with mining depth and methane permeability decreases correspondingly. Methane extraction before coal mining lowers mine temperature and thus enhances permeability near working faces. On the other hand, coal seams can reach yield deformation more easily and even induce stress sharp drop or failure in higher temperature environments. The combined effect of stress, pore pressure and temperature might easily trigger a rapid enhancement of permeability near working faces or even coal and gas outbursts. Therefore, understanding this combined effect on methane permeability is a key issue to hazard detection and mitigation. So far, this combined effect has not been well understood in either experimental measurements or numerical simulations. This paper investigated the methane permeability of six gas-containing coal samples in a complete stress–strain process through our thermal-hydro-mechanical (THM) coupled test apparatus. In these tests, coal specimens were taken from the anthracite coals of Sihe colliery and Zhaozhuang colliery within the southeast Qinshui Basin in Shanxi province of China. A self-made ‘THM coupled with triaxial servo-controlled seepage apparatus for containing-gas coal’ was developed for these tests. The evolution of methane permeability in a complete stress–strain process was continuously measured under constant differential gas pressure, constant confining pressure and three constant temperatures of 30, 50 and \(70\,^{\circ }\hbox {C}\). These experimental results revealed that: (1) Higher temperature had lower compressive strength and lower limit strain, thus coal seams more easily failed. (2) The evolution of methane permeability of coal heavily depended on stress–strain stages. The permeability decreased with the increase of deviatoric stress at the initial compaction and elastic deformation stages, while it increased with the increase of deviatoric stress at the stages of yield deformation, stress sharp drop and residual stress. (3) Temperature effect on the permeability of coal varied with deformation stages, too. This effect was significant before yield deformation, where higher temperature caused lower permeability, but not important after yield deformation, at which the development of coal cracks became dominant. These observations and measurements are helpful for the design of hazards detection and mitigation measures during coal mining process.