Understanding the interaction between groundwater and surface water in permafrost regions is essential to study flood frequencies and river water quality, especially in the high latitude/altitude basins. The application of heat tracing method, based on oscillating streatnbed temperature signals, is a promising geophysical method for identifying and quantifying the interaction between groundwater and surface water. Analytical analysis based on a one-dimensional convective -conductive heat transport equation combined with the fiber-optic distributed temperature sensing method was applied on a stream bed of a mountainous permafrost region in the Yeniugou Basin, located in the upper Heihe River on the northern Tibetan Plateau. The results indicated that low connectivity existed the stream and groundwater in permafrost regions. The interaction between surface water and groundwater increased with the thawing of the active layer. This study demonstrates that the heat tracing method can be applied to study surface water-groundwater interaction over temporal and spatial scales in permafrost regions.