Field monitoring of water quality during the autumn flood season in the middle and lower reaches of the Yellow River in 2021 was carried out. During this period, a host of methods, including the single-factor evaluation method, index evaluation method, and fuzzy mathematics method, were utilized to evaluate the water quality status. The relevant findings indicate that the water quality of the mainstream and tributaries in the middle and lower reaches of the Yellow River in the autumn flood season is excellent, which meets the water function zoning and water quality goals. In particular, the single-factor evaluation method emphasizes the use of the single index with the most serious pollution to represent the comprehensive water quality category, whereas the fuzzy mathematics method uses the multi-factor contribution rate to calculate the membership degree of water quality. Therefore, it is superior to the single-factor evaluation method in determining the water quality of the water functional zones within the evaluation scope. Meanwhile, the Nemerow index of the water quality of the tributaries of Yiluo River and Qinhe River at the section entering the Yellow River is lower than that of the mainstream, indicating that the water quality of tributaries is better than that of the mainstream during the monitoring period. Overall, the results of this research are conducive to the objective evaluation of the water quality of the Yellow River during the autumn flood season, thus providing more scientific technical support for the ecological conservation and restoration of the Yellow River basin.