The invention relates to a watershed-scale hydrological nonconformity diagnosis method. The method includes the following steps that: a watershed non-uniform indicator system is built; nonconformity diagnosis is performed on single indicator sequences; and watershed hydrological nonconformity quantitative diagnosis is performed. According to the method, the indicator sequences representing the developmental characteristics of hydrological processes are screened out, and the indicator sequences are classified and combined according to an indicator-element-target level; whether the sequences are in trend variation states or jump variation states can be judged on the whole; after nonconformity diagnosis is performed on each single indicator sequence, comprehensive nonconformity diagnosis is performed on each indicator, and therefore, defects in corresponding aspects in the prior art can be avoided; and nonconformity judgment is performed on the plurality of indicators with the same standard, and therefore, theoretical support can be provided for a plurality of kinds of application, such as water resource diagnosis, reservoir dispatching, water conservancy engineering design, flood control and fight against drought.