The invention discloses a logistic regression-based aircraft flutter analysis and QMU evaluation method, and relates to a quantification technology of uncertainties and margins. The method comprises the following steps of 1) establishing a database of existing flight tests, namely whether the flight test suffers from flutter or not under a certain group of designed parameters, recording flutter as 1 and recording non-flutter as 0; 2) establishing a regression prediction model; 3) fitting a regression coefficient; 4) predicting the model; and 5) performing QMU evaluation. By omitting a complex finite element analysis process, high calculating efficiency and convenient operation are realized, and the method is applicable to the field where it is difficult to perform numerical value simulation on flutter and the like of a hypersonic thermal structure; the analysis result is evaluated by the QMU, and uncertainties of the flutter speed and flutter border are taken into consideration at the same time, so that security criterion for a flutter problem is high in credibility; and flutter probability of an aircraft under a certain designed variable condition can be predicted, so that the method can be used for assisting aircraft design.