The invention discloses a drainage basin water quality comprehensive evaluation method and system. A water quality comprehensive evaluation analysis model and a credibility distribution function are built, and a water quality index monitoring value is converted into the credibility of each evaluation level; on the basis of evidential reasoning combination rules and algorithms, indexes belonging tothe same evaluation level are subjected to evidence recursion synthesis, and probability distribution of each evaluation level is worked out; the utility theory is introduced, and water quality comparison is achieved. By building the water quality comprehensive evaluation analysis model and the credibility distribution function, water quality monitoring data normalization processing is achieved,the damage caused by a scoring method to source data information is avoided, processing of index monitoring values is more scientific and accurate, and the water quality condition can be better reflected; by adopting the evidential reasoning combination rules and the evidential reasoning algorithms, multi-index and multi-evaluation-level evidence synthesis is achieved, uncertain information processing is sufficiently considered, and the evaluation result better conforms to the actual condition.