In order to evaluate and analyze the water quality of Yiyuan County，24 indexes，including fluoride，iodide，manganese and plumbum，in the water quality data of 15 monitoring points in Yiyuan county were selected，and the water quality evaluation and comparison are conducted by the improved fuzzy comprehensive evaluation method and Nemero index method． The results of the improved fuzzy comprehensive evaluation consider the degree of membership of different factors in different water quality categories． On this basis，the results are improved in algorithm to ensure that the results are continuous． The improved Nemero index method considers the effect of the maximum value on the overall water quality，and the weight factor is added to balance the results． There is an obvious change． The trend of water quality evaluation of Yiyuan County in wet season is basically the same as that in dry season． The main factors affecting the groundwater quality in Yiyuan County are summarized by principal component analysis，which are mainly the influence of the elements contained in the formation， the excessive use of artificial pesticides and chemical fertilizers，the improper treatment of animal manure，the improper discharge of factory waste water and dust，and so on． The water rock interaction in the study area is mainly the dissolution and sedimentation，and a few mixed effects．