The invention discloses a multi-operating-condition failure load based composite structure uncertainty optimization method. The method includes steps: (1) subjecting an established finite element model to model correction and confirmation under an uncertainty condition; (2) subjecting a composite to safety coefficient based two-stage optimization, wherein first-stage optimization refers to composite super layer optimization aiming at structural weight, and second-stage optimization refers to stacking sequence optimization aiming at structural bearing capacity; (3) on the basis of an uncertainty parameter range quantified in the step (1), performing bearing capacity reliability analysis on a scheme optimized in the step (2) to obtain reliability of structure bearing capacity under differentoperating conditions; (4) subjecting the composite to reliability based optimization, taking bearing reliability of the scheme optimized in the step (3) as a constraint pair, performing super layer optimization aiming at weight reduction, and performing second-stage stacking sequence optimization aiming at structure bearing capacity lower bound maximization.