An aircraft model modification system based on modal test data comprises a core data structure module, a CAE data import module, a test data import module, a three-dimensional display module, an MAC matrix calculation module, a three-dimensional MAC matrix display module, a finite element model updating solution module and a model modification module. The aircraft model modification system achieves comparison validation and finite element model modification of finite element analysis results and test results, improves model modification efficiency, and enhances comprehensiveness and accuracy of virtual tests.