The invention belongs to the field of hydropower scheduling and discloses a multi-small-hydropower-group output uncertainty analysis method based on scenario analysis. For the features of randomness and difficult prediction of small hydropower output, a random planning correlation theory is introduced, an output scenario set is constructed by use of a scenario analysis method, fuzzy cluster and cluster integrated quality methods are brought forward for realizing scenario reduction, condition probability distribution of small hydropower prediction and an actual scenario under a current prediction precision condition is established, and small hydropower uncertainties are converted into finite uncertainty condition scenario problems. At the same time, for the situation where multiple small hydropower groups are accessed to a power grid, generating feature differences between the small hydropower groups are taken into consideration, and a multi-small-hydropower-group scenario combination is determined by application of a mathematical combination theory. This is taken as an input condition for compiling a hydropower plan, the accuracy and the performability of the hydropower plan can be improved, and the method has an important utility value especially for hydropower scheduling of a region rich in small hydropower.