The estimation of the posterior probability density function (PDF) of unknown parameters remains a challenge in stochastic nonlinear model updating with uncertainties; thus, a novel Bayesian inference framework based on the Gaussian process metamodel (GPM) and the advanced Markov chain Monte Carlo (MCMC) method is proposed in this paper. The instantaneous characteristics (ICs) of the decomposed measurement response, calculated using the Hilbert transform and the discrete analytical mode decomposition methodology, are extracted as nonlinear indices and further used to construct the likelihood function. Then, the posterior PDFs of structural nonlinear model parameters are derived based on the Bayesian theorem. To precisely calculate the posterior PDF, an advanced MCMC approach, i.e., delayed rejection adaptive Metropolis-Hastings (DRAM) algorithm, is adopted with the advantages of a high acceptance ratio and strong robustness. However, as a common shortage in most MCMC methods, the resampling technology is still applied, and numerous iterations of nonlinear simulations are conducted to ensure accuracy, thus directly reducing the computational efficiency of the DRAM. To address the abovementioned issue, a mathematical regression metamodel of the GPM with a polynomial kernel function is adopted in this paper instead of the traditional finite element model (FEM) to simulate a nonlinear response for the reduction of computational cost, and the hyperparameters are further estimated using the conjugate gradient optimization methodology. Finally, numerical simulations concerning a Giuffré–Menegotto–Pinto modeled steel-frame structure and a seven-storey base-isolated structure are conducted. Furthermore, a shake-table experimental test of a nonlinear steel framework is investigated to validate the accuracy of the Bayesian inference method. Both simulations and experiment demonstrate that the proposed GPM and DRAM-based Bayesian method effectively estimates the posterior PDF of unknown parameters and is appropriate for stochastic nonlinear model updating even with multisource uncertainties.