Whole index evaluation method and double index evaluation method were applied to evaluate the water quality compliance rates of 4493 national water function zones in China. The results show that there are clear differences between the two evaluation methods, with 61. 2% and 49. 6% water quality compliance rate respectively. The evaluation result of double index evaluation method is better than that of whole index evaluation method. According to the relationship between the pollution capacity of water function zone and measured amount of pollutants into rivers, the bearing capacity of water function zones were analyzed. The results show that 2907 water function zones are not overloaded with the rate of 64. 7%, while the other 35. 3% of the national water function zones has taken more than 60% of the total amount of pollutants within 25% of the total amount of pollution capacity, showing that pollution has been overloaded but water quality reach the standards in some water function zones. It can be explained as the calculation standard of pollutant carrying capacity tends to be strict. In the meantime, there is another kind of problem that pollution has not been overloaded but water quality is not up to the standard, which can be explained as the high value of the background pollutants, affected by pollutants exceeding the standard into rivers of upstream function area, and lacking of complete measurement of agricultural non-point source pollution for the time being.