In order to solve the general evaluation shortcomings of the fuzzy recognition theory on 5 level standard values and the maximum membership degree principle, this study puts forward the calculation method of 6 level water quality to improve the model of fuzzy pattern recognition, furthermore, the Pair Analysis Set (SPA) theory was introduced to deal with the uncertainty information between the different standard levels, then the fuzzy pattern recognition model was established to be applied in river systems. The evaluation results showed that the 6 level fuzzy pattern recognition model based on SPA was more accurate to determine the water quality comprehensive grade, which could provide theoretical support for the treatment of river water pollution.