The Fuzzy Comprehensive Evaluation (FCE) and the Principal Component Analysis (PCA) were simulated to assess water quality of the Nansi Lake Basin, China. The membership functions were established via the Nor-Half Sinusoidal Distribution Method, and the weight was calculated via the Exceeding Standard Multiple Method. To enhance the efficiency of extracting principal pollutant, the eigenequation was solved through the Jacobi Method, and the principal components were extracted based on eigenvalue, contribution ratio, accumulating contribution ratio, principal component loading and score. Water quality classification based on “National Surface Water Environmental Quality Standards of China (GB3838-2002) was used to assess the water quality. Considering the difference of the temporal and spatial distribution in average, water quality of Level I was 28.9%, 28.1%, 25.1%, 25.6%, respectively in spring, summer, autumn, and winter, which suggested that water quality in spring and summer was better than in autumn and winter. The order of water quality was Zhaoyang Lake (Level I) > Nanyang Lake (Level I) > Dushan Lake (Level III) > Weishan Lake (Level III and IV). There were four extracted principal components that can replace the fourteen pollutant indexes for assessing water quality. According to the annual mean data of the 1st principal components, the most important pollutions were heavy metals, including As (0.933), Hg (0.931), Cd (0.929), Cr(VI) (0.926), Pb (0.925), and Cu (0.534). It is proved that the combined FCE-PCA model could provide valuable information in the water quality assessment for the Nansi Lake Basin.