In the vibration analysis of joined conical-cylindrical shells, mode methods are widely used. However, from the practical results, boundary conditions affect significantly on the vibration behaviors of these structures. Therefore, the assumed modes may not obtain accurate results, which is terrible for structural design or vibration control. Finite element method (FEM) can be used to solve such problems, whereas the time and hardware costs are unacceptable, especially for the structural design and vibration control. The Craig-Bampton (C-B) method takes into account the advantages of both FEM and mode theory, and is very suitable for the dynamic analysis. This paper studies the advantages and feasibility of the C-B method in vibration analysis of joined conical-cylindrical shells. Using the eight-node super-parametric shell element and Hamilton's principle, the finite element equation of motion for the joined conical-cylindrical shell is established. The reduced FE model of the structure is obtained by using the C-B method. A process for efficient structural dynamic design is proposed. The correctness of the model reduction based on C-B method is verified through modal measurement experiments. In addition, some examples are given to illustrate the advantages of the C-B method in the optimization design and dynamic analysis of joined conical-cylindrical shell structures. Finally, a solution idea of coordinate transformation matrix is proposed when there are much more interfaces between substructures.