The invention discloses a multi-scale composite material structure local fatigue evaluation method and system. The evaluation method includes acquiring a beam structure parameter of a one-dimensionalbeam structure; acquiring a plate structure parameter of a two-dimensional plate structure; determining a vibration differential equation to be identified according to the beam structure parameter andthe plate structure parameter; determining an objective function according to the vibration differential equation; determining a local fatigue damage factor according to the objective function; and evaluating a fatigue state of a composite material structure according to the local fatigue damage factor. By the adoption of the evaluation method and system, an earlier composite material state can be evaluated by use of non-destructive and in-situ detection means, and the local fatigue state of the composite material structure is characterized.