The uncertainty in parameter estimation arises from structural systems’ input and output measured errors and from structural model errors. An experimental verification of the shuffled complex evolution metropolis algorithm (SCEM-UA) for identifying the optimal parameters of structural systems and estimating their uncertainty is presented. First, the estimation framework is theoretically developed. The SCEM-UA algorithm is employed to search through feasible parameters’ space and to infer the posterior distribution of the parameters automatically. The resulting posterior parameter distribution then provides the most likely estimation of parameter sets that produces the best model performance. The algorithm is subsequently validated through both numerical simulation and shaking table experiment for estimating the parameters of structural systems considering the uncertainty of available information. Finally, the proposed algorithm is extended to identify the uncertain physical parameters of a nonlinear structural system with a particle mass tuned damper (PTMD). The results demonstrate that the proposed algorithm can effectively estimate parameters with uncertainty for nonlinear structural systems, and it has a stronger anti-noise capability. Notably, the SCEM-UA method not only shows better global optimization capability compared with other heuristic optimization methods, but it also has the ability to simultaneously estimate the uncertainties associated with the posterior distributions of the structural parameters within a single optimization run.