The alpine mountain areas are the origins of runoff. Runoff in most of the rivers in the mountain areas, is mainly from melt-waters of snowpacks and glaciers, and/ or from rainfall in alpine mountain areas. Base flow is the main component of runoff, particularly during low flow periods, no matter what types of runoff generation. To carry out the simulation of base flow process for different runoff generation from rainfall, snow and/or glacier, has a significant meaning for the basin water resources management and the river health maintenance. However, reliable separation of base flow under different hydrological conditions is the key problem. The nonlinear aquifer storage-discharge approach will be used in the study, which has a physical meaning with only two parameters and is easy to parameterize. The parameters in the exponential function that describes the aquifer storage-discharge relationship could be optimized independent of the SWAT model by using observed streamflow data during recession periods. The functions of base flow calculation will be constructed based on the aquifer storage-discharge relationship and the methods of base flow simulation in the distributed hydrological model under different hydrological conditions will be developed. Moreover, the equations of the digital filter used for base flow separation applicable for the basins dominated by snowmelt and glacier melt will be developed, which is based in signal analysis and processing for rainfall-dominated basins. By collecting the data, the improved model will be established for the typical catchments in the Manas River Basin (dominated by snow/ glacier melt) in the arid-cold mountain areas, Shaying River Basin (dominated by rainfall) in the semi humid-humid areas, and will be calibrated, validated and assessed. Based on the simulation by the improved model, the spatial and temporal variations in base flow will be analyzed, the mechanism will be discussed, the contribution of base flow to runoff will be quantified, and the similarities and differences of the base flow characteristics between the arid-cold mountain areas and semi humid-humid areas will be revealed.