The drought-flood abrupt alternation (DFAA), defined as the phenomenon of flood (drought) following droughts (flood), magnifies the impact of individual flood and drought events yet has not been accurate assessment. Previous studies have used the stationary approach to identify DFAA events, where a fixed parameter is used to fit the SSI and then a threshold is determined to identify DFAA events. However, because changes in climate or human activities can induce significant variations in the underlying probability distributions of streamflow, the method’s usual assumption of stationarity should be questioned. In this study, a new non-stationary assessment framework considering natural-social systems is developed for identifying hydrological DFAA events. The framework was applied to the study of DFAA events at Huayuankou Station (HYK) in the Yellow River Basin (YRB) over the past 60 years (1961–2020). The main findings include: (1) The non-stationary test results demonstrate the emergence of non-stationary characteristics of streamflow at HYK station. The study period is divided into two periods, the base period (1961–1990) and the change period (1991–2020), based on the mutation test results. (2) the climate and anthropogenic factors screened based on the causal inference method can effectively improve the fitting performance of the non-stationary model of the streamflow at the HYK station, and better respond to the evolutionary characteristics under the changing environments of the extreme hydrological events; and a new sedimentation-based reservoir index (SDRI) considering reservoir siltation has been developed, which has less uncertainty than fitting reservoir index (RI) as a covariate. (3) The trends of DFAA events identified by non-stationary standardized streamflow index (NSSI) and standardized streamflow index (SSI) are consistent. However, the frequency and severity of DFAA events may be underestimated if the non-stationary characteristics of streamflow are not considered. (4) The frequency and severity of DFAA events at HYK station during the change period were higher than those during the base period. In conclusion, the above findings contribute to a better understanding of the effect of streamflow non-stationary on DFAA event identification and can provide valuable information for drought and flood management decisions in changing environments.