Analytical solutions for vibration analysis of the rods with variable cross section are in general complex and in many cases impossible. On the other hand, approximate methods such as the weighted residual, Rayleigh-Ritz and finite difference methods also have their own shortcomings such as a limited number of natural frequencies and accuracy. Using the wave propagation method, the structure is partitioned into several continuous segments with constant cross-section, for which there exists an exact analytical solution. Waves in positive and negative directions at the entrance of each segment are obtained in terms of waves at the initial segment. Then, by satisfying the boundary conditions, the characteristic equation is obtained and all natural frequencies are calculated. By adding waves in positive and negative directions at each point, the shape modes are obtained. To verify this modified method, the frequencies and mode shapes of a rod with polynomial cross section, which has an exact analytical solution, are compared and have proven to be of highly accuracy. Therefore, this method can also be used to calculate the natural frequencies and its mode shapes of the rods with variable cross section for which no analytical solution is available.