In this paper, a novel and efficient modal analysis method is raised to work on blisk structures based on mixed-dimension finite element model (MDFEM). The blade and the disk are modeled separately. The blade model is figured by 3D solid elements considering its complex configuration and its degrees-of-freedom (DOFs) are condensed by dynamic substructural method. Meanwhile, the disk is structured by 2D axisymmetric element developed specially in this paper. The DOFs of entire blisk are tremendously reduced by this modeling approach. The key idea of this method is derivation of displacement compatibility to different dimensional models. Mechanical energy equivalence and summation further contribute to the model synthesis and modal analysis of blade and disk. This method has been successfully applied on the modal analysis of blisk structures in turbine, which reveals its effectiveness and proves that this method reduces the computational time expenses while maintaining the precision performances of full 3D model. Though there is limitation that structure should have proper coverage of blades, this method is still feasible for most blisks in engineering practice.