Baseflow is an important component of runoff. Investigation on the baseflow separation methods is of significance for realizinghydrological cycle and water resources management in cold and arid regions. The Heihe River Basin is located in typicalcold and arid regions in the Northwest China. Based on the observed runoff time series from 1954 to 2012 at the Yingluoxia station,one of the hydrological stations in the upper reaches of the Heihe River,the suitability of the 9 baseflow separation methods in theHeihe River Basin was analyzed,including digital filtering, BFI and HYSEP methods. The results show that: (1) the inner-annual baseflowtrends estimated with the 9 kinds of methods notably conform to the characteristics of the Heihe River Basin, but the baseflow separationresults are significantly affected by the precipitation in different months; (2) both BFI and HYSEP can better identify the baseflow processof different years,the average annual baseflow indices of B1, B2 and H3 are close to the isotope results, and the statistics of annualbaseflow indices with the 9 baseflow separation methods show that the baseflow sequences are relatively smooth and gently decadalvariation; (3) the baseflow and duration curve estimated by H3 can objectively reflect the recession hydrograph,and the determinationcoefficients between H3 and constant-slope separation method are superior to other methods (R2=0.825，p<0.001). From the aboveanalysis, H3 is expected as the most suitable baseflow separation method for the upper reaches of the Heihe River, which can give a comprehensiveconsideration of the inner-annual baseflow trends, annual index stability and process curve rationality.