Abstract: The calculation method and model of the basic ecological instream flow threshold were proposed considering hydrological alterations under non-stationary, and applied to the Xining section of the Huang River for illustration. Mann-Kendal test and sliding t test were used for comprehensive diagnosis of hydrological alterations under non-stationary. After restoration and correction, the natural flow process before hydrological alterations was used as the benchmark, and the Generalized Extreme Value Distribution (GEV) flow mode method, the diachronic curve method, and the improved equal frequency method within one year were used to calculate the ecological flow process in the river. The threshold of basic ecological flow in the river was the outsourcing line of the calculation results of the above method. The results show that the abrupt change point of the annual runoff time series of Xining Station is 2000. After reduction and correction, natural runoff data were used to calculate basic ecological flow threshold. Basic ecological flow lower threshold averages of Xining Station are 11.0 m³/s in drought period, 17.6 m³/s in common water period, and 27.5 m³/s in flood period, respectively. The upper threshold averages are 17.0 m³/s in drought period, 35.6 m³/s in common water period, and 56.0 m³/s in flood period, respectively. Comparing with the existing results, the calculation method of basic ecological flow threshold has a certain rationality, and it is closer to the hydrological ecosystem of the mainstream of the Huang River with seasonality.