There are few studies on the hydrological characteristics on the landscape zone scale in alpine cold region at present. This paper aimed to identify the spatial and temporal variations in the origin and composition of the runoff, and to reveal the hydrological characteristics in each zone, based on the isotopic analysis of glacier, snow, frozen soil, groundwater, etc. The results showed that during the wet season, heavy precipitation and high temperature in the Mafengou River basin caused secondary evaporation which led to isotope fractionation effects. Therefore, the isotope values remained high. Temperature effects were significant. During the dry season, the temperature was low. Precipitation was in the solid state during the cold season and the evaporation was weak. Water vapor came from the evaporation of local water bodies. Therefore, less secondary evaporation and water vapor exchange occurred, leading to negative values of delta18O and deltaD. delta18O and deltaD values of precipitation and various water bodies exhibited strong seasonal variations. Precipitation exhibited altitude effects, delta18O = -0. 005 2H - 8. 951, deltaD = -0.018 5H - 34. 873. Other water bodies did not show altitude effects in the wet season and dry season, because the runoff was not only recharged by precipitation, but also influenced by the freezing and thawing process of the glacier, snow and frozen soil. The mutual transformation of precipitation, melt water, surface water and groundwater led to variations in isotopic composition. Therefore, homogenization and evaporation effect are the main control factors of isotope variations.