This paper presents two approaches to the stability analysis of flexible dynamical systems in the time domain. The first is based on the partial Floquet theory and proceeds in three steps. A preprocessing step evaluates optimized signals based on the proper orthogonal decomposition (POD) method. Next, the system stability characteristics are obtained from partial Floquet theory through singular value decomposition (SVD). Finally, a postprocessing step assesses the accuracy of the identified stability characteristics. The Lyapunov characteristic exponent (LCE) theory provides the theoretical background for the second approach. It is shown that the system stability characteristics are related to the LCE closely, for both constant and periodic coefficient systems. For the latter systems, an exponential approximation is proposed to evaluate the transition matrix. Numerical simulations show that the proposed approaches are robust enough to deal with the stability analysis of flexible dynamical systems and the predictions of the two approaches are found to be in close agreement.