AbstractQuality and stability are the basic characteristics of ecosystems, reflecting their structure, process, functional integrity, ability to resist disturbance, self‐regulation, and dynamic balance. The quantitative description of ecosystem quality and stability is an indispensable and important task to promote the ecological protection and high‐quality development of the Yellow River Basin as a major national strategy. In this study, an index evaluation system was constructed from the perspective of system governance, considering the special characteristics of the Yellow River Basin, and an entropy weight model was used to establish a multi‐indicator long time series ecosystem quality evaluation index (EQI) to quantitatively describe the ecological quality changes in the Yellow River Basin over 40 years. The dissipative structure theory and Brussels apparatus model were used to establish quantitative indicators and methods, and provide ideas for the study of ecosystem homeostasis transformation in the Yellow River basin. This study found that: (1) the average EQI value of the Yellow River Basin ecosystem for 40 years was 63.96, the maximum and minimum values were 69.65 and 59.45, respectively; the overall quality showed an oscillating trend of improvement, with an annual increase of 0.03, and the spatial distribution was better in the downstream than in the midstream, and in the midstream than in the upstream; (2) The key factors influencing the system changed gradually from the total water consumption and total annual precipitation in the basin in the early stage to the average income of residents in the last 10 years. (3) The system steady‐state transition force values from 1980 to 2019 were all <0, the steady‐state conversion force of the Yellow River Basin ecosystem was low, but the overall trend was oscillating upward, and the overall trend was getting closer to the critical condition of steady‐state conversion.