The invention discloses a complex structure finite element model correction method based on multi-stage super units, which comprises the following steps of establishing an initial finite element model, and dividing the initial finite element model into multi-stage super unit finite element models; carrying out condensation polymerization on the multi-stage super-unit model by adopting a modal synthesis method, carrying out condensation polymerization on the super-units to obtain a mass matrix and a rigidity matrix, assembling the obtained mass matrix and the obtained rigidity matrix to a residual structure, and carrying out modal analysis on the residual structure to obtain a modal shape and an inherent frequency; and measuring a test mode of an actual structure, constructing a residual error of a test inherent frequency and the inherent frequency obtained by modal analysis by adopting a perturbation method, establishing an objective function, and realizing the model correction by optimizing a reverse problem solution. According to the present invention, on the basis of the initial finite element model, the multi-stage super-unit modeling analysis is firstly carried out, and an appropriate structure is selected as the residual structure, and the modal analysis is carried out on the residual structure, and the model correction is carried out on the residual structure, so that the finite element model correction efficiency is effectively improved.