Different assessment results may be obtained through annual average method and frequency method evaluating water function zones with same water quality data, during water function area compliance evaluation work. In order to choose the evaluation method scientifically and reasonably, Mathematical statistics analysis methods including Pearson Ⅲ curve was introduced and the characteristic of water quality monitoring data was analyzed. In the end, the applying conditions and range of annual average method and frequency method are acquired. When the water quality data meeting CvCs≤0. 5, Cs≤2, annual average method should be applied, otherwise frequency method should be chosen. Two case studies have been conducted in the northern Daling River basin and the southern Tuojiang River basin, respectively, to verify the conclusion. The contradiction between the evaluation results of different methods is solved, providing strong basis for water resource management and planning.