To study the influences of geo-temperature on the seepage properties of a shale, we analyzed the temperature-dependent patterns of viscous force change of methane, the formations of a shale by heat stress and expansion, and the matrix shrinkage caused by methane desorption. By using shale samples of Longmaxi Formation in Youyang of Southeast Chongqing, we conducted an experiment on the temperature dependence of the seepage of shale rock. The experiment shows that an increase in temperature leads to an increased viscous force of methane and reduced flow speed. The differences in expansion of clay minerals and organic matters produce thermal stress and compress the shale skeleton, and matrix thermal expansion reduces the substrate gaps, both leading to a decrease in the seepage channels. The matrix shrinkage has very little influence on the infiltration capacity of pores and cracks. The major effects of temperature on the seepage characteristics of shale are the decrease of flow speed of methane due to increased viscous force and compressed seepage channels due to thermal stress and thermal expansion.