In order to study the water quality and its changing trend of the Yangtze river(YR) and according to the eight-index measured data on 103 government-control sections of YR from 2006 to 2010 (total 515 samples) and the standards of quality evaluation of groundwater,the paper established the projection pursuit clustering model of comprehensive evaluation of water quality. The results show that the water quality on the control sections is quite good, the water quality of type I and Ⅱ take up 60% and 22.7% respectively. The water quality in upperstream is better than that in downstream. The water pollution is quite serious in the Chemical-industry developed areas. From 2006 to 2009, the water quality was gradually improved year by year,and was the worst in 2010. The paper researched the rule of influence of cutoff radius R value (CRRV) on the results of PPC model . The theory analysis show that the scheme of taking the smaller CRRV (R=0.1 Sz) is absolutely unreasonable, the larger CRRV (rmax≤R≤2p) is error, should not be the constant, and only the moderate-suitable value of CRRV (rmax/5≤R≤rmax/3) is reasonable correct.