This paper presents a Fourier spectral element method (FSEM) to analyze the free vibration of conical-cylindrical-spherical shells with arbitrary boundary conditions. Cylindrical-conical and cylindrical-spherical shells as special cases are also considered. In this method, each fundamental shell component (i.e., cylindrical, conical, and spherical shells) is divided into appropriate elements. The variational principle in conjunction with first-order shear deformation shell theory is employed to model the shell elements. Since the displacement and rotation components of each element are expressed as a linear superposition of nodeless Fourier sine functions and nodal Lagrangian polynomials, the global equations of the coupled shell structure can be obtained by adopting the assembly procedure. The Fourier sine series in the displacement field is introduced to enhance the accuracy and convergence of the solution. Numerical results show that the FSEM can be effectively applied to vibration analysis of the coupled shell structures. Numerous results for coupled shell structures with general boundary conditions are presented. Furthermore, the effects of geometric parameters and boundary conditions on the frequencies are investigated.