Growing interests in simulating changes in hydrological processes on global and regional scales have been raised by more frequent strong floods and droughts on the global scale induced by climate change, which would have significant impacts on social and economic systems, food security and the survival and development of humans. General circulation models (GCMs) perform reasonably well in simulating current climate in terms of annual or seasonal averages on large spatial scales, thereby showing the capability to provide inputs for studies associated with hydrological responses to climate change on continental or global scale. However, the models perform poorly on small spatial and time scales relevant to regional impact analysis. The Statistical Downscaling Model (SDSM) is considered a very useful tool to address spatial-matching problems. It enables the study of climate change response to be carried out on local scales. In this paper, the applicability of SDSM in the Bosten Lake Basin was evaluated and the model was used to analyze the trends in future maximum and minimum temperature in this watershed. First, maximum temperature and minimum temperature were selected as the predictands. Appropriate meso-scale atmospheric variables were selected as downscaling predictors. Then, a statistical transfer function between them was constructed by the United States National Centers for Environmental Prediction (NCEP) re-analysis data set and observations at four stations. The first 30 years (1961–1990) of the obtained data series (1961–2001) was used to calibrate the model, while the remaining ten years (1991–2001) of data series was used to validate the model. The results show good agreement between the observations and the outputs from the model. On the basis of this, with the outputs of Hadley Centre Coupled Model, version 3 (HadCM3) under A2 and B2 scenarios respectively, the calibrated SDSM model generated future daily temperature series, which were subsequently used to analyze the temporal trends. The results show that there is an obvious increasing trend for the future maximum temperature and minimum temperature in the Bosten Lake Basin on daily, monthly, seasonal and yearly scales, respectively. The increase in the A2 scenario is larger than in the B2 scenario. The largest increase was found in summer while the smallest was in winter. This study would provide a scientific basis for further study of climate change over the Bosten Lake Basin.