Watersheds in cold regions are undergoing climate warming and permafrost degradation, which result in quantitative shifts in surface water–groundwater interaction. Daily discharge, annual maximum frozen depth (AMFD) of seasonal frozen soil, precipitation and negative degree-day temperature were analyzed to explore changes and correlations of climate, runoff and permafrost in the Upper Yellow River Basin from 1980 to 2009. Plausible permafrost degradation trends were found at two of the stations, but an unsubstantiated trend was found at Huangheyan Station. The winter recession processes slowed down gradually from 1980 to 2009 at three stations but had little relation to AMFD. Meanwhile, the ratio of monthly maximum to minimum discharge reduced significantly. It is clear that permafrost degradation and runoff variations have already occurred in the basin, particularly in zones where the permafrost coverage is above 40%. It is proposed that the variations in the hydrological regimes were caused by permafrost degradation which enlarged infiltration and sub-surface water contribution to winter discharge. The differences of changes in runoff generation and confluence in various regions were thought to be affected by different permafrost coverage and changes because the exchange of groundwater and surface-water mediated by permafrost.