A highly efficient probabilistic framework of finite element model updating in the presence of measurement noise/uncertainty using intelligent inference is presented. This framework uses incomplete modal measurement information as input and is built upon the Bayesian inference approach. To alleviate the computational cost, Metropolis–Hastings Markov chain Monte Carlo (MH MCMC) is adopted to reduce the size of samples required for repeated finite element modal analyses. Since adopting such a sampling technique in Bayesian model updating usually yields a sparse posterior probability density function (PDF) over the reduced parametric space, Gaussian process (GP) is then incorporated in order to enrich analysis results that can lead to a comprehensive posterior PDF. The PDF obtained with densely distributed data points allows us to find the most optimal model parameters with high fidelity. To facilitate the entire model updating process with automation, the algorithm is implemented under ansys Parametric Design Language (apdl) in ansys environment. The effectiveness of the new framework is demonstrated via systematic case studies.