The wave-based method (WBM) is a feasible method which investigates the free vibration characteristics of orthotropic cylindrical shells under general boundary conditions. Based on Reissner–Naghid’s shell theory, the governing motion equation is established, and the displacement variables are transformed into wave functions formed to satisfy the governing equations. On the basis of the kinematic relationship between the force resultant and displacement vector, the overall matrix of the shell is established. Comparison studies of this paper with the solutions in the literatures were carried out to validate the accuracy of the present method. Furthermore, by analyzing some numerical examples, the free vibration characteristics of orthogonal anisotropic cylindrical shells under classical boundary conditions, elastic boundary conditions, and their combinations are studied. Also, the effects of the material parameter and geometric constant on the natural frequencies for the orthotropic circular cylindrical shell under general boundary conditions are discussed. The conclusions obtained can be used as data reference for future calculation methods.