In order to try the use of matter element analysis method in water quality assessment of the Yellow River, the paper used matter element analysis method to evaluate water quality of the Yellow River, and compared the results with that of conventional single factor index method. The results showed that the assessment results of two methods were very different, the water quality evaluated by matter element analysis method was better than that by the single factor index method, the difference are caused by the different view point of two evaluation methods. Single factor index method is to reflect the veto right of single factor, and the matter element analysis method is to reflect the comprehensive effects of different evaluation factors on water quality. The result of matter element analysis method is more comprehensive, system, reality.