The free and forced vibration analysis of the FGM double-layered submarine type coupled structure with elastic boundary conditions and coupled connection conditions is presented by using the spectral geometry method. The displacement variables of substructures are represented in the uniform form, and the displacement components of individual structures are represented by the spectral geometry series. Multiple sets of boundary springs are introduced at the coupling interfaces and end boundaries between the substructures, and the elastic and rigid coupling and boundary conditions can be easily obtained by assigning certain values to the stiffness of the artificial springs. The Rayleigh-Ritz procedure is used to obtain the natural frequencies of the structure as well as the frequency response under forced vibration. The convergence of the method is verified by numerical arithmetic examples, and the results of the natural frequencies and frequency response obtained by comparing the finite element methods are used to demonstrate the good accuracy and reliability of the present method. Finally, some parametric analysis studies are carried out for FGM double-layered submarine type coupled structures with different boundaries, dimensions, and material parameters.