The proposed method of permafrost distribution mapping entails the use of a computer-based model that takes into account the specific conditions of arid mountains for permafrost formation and occurrence. In the intracontinental arid mountains, incoming short-wave solar radiation, mean annual temperature and evaporation are the main influences on the distribution of permafrost. Coarse debris is widespread in the high mountains and greatly influences the thermal state of the ground. The model can compute heat transfer in the coarse debris, which is considered a porous body, and it can be used for permafrost distribution mapping with various degrees of spatial resolution. As a result, the GIS-based map of permafrost distribution for the Bolshaya Almatinka River basin, Kazakhstan, was generated.