This work simulates a laboratory-scale three-dimensional methane/air burner, which features a bluff body stabilized, lean partially premixed flame experiencing strong limit cycle oscillations. A thin steel liner is installed around the combustion chamber, which heavily interacts with the flow field and produces large amplitude structural deformation via fluid–structure interaction (FSI). An unsteady Reynolds averaged Navier–Stokes (URANS) approach uses the shear stress transport (SST) turbulence model and a flamelet generated manifold (FGM) combustion model to predict the thermoacoustic oscillations in the turbulent reacting flow. The solver also has a built-in finite element structure model, which solves the structural governing equations simultaneously with the computational fluid dynamics (CFD)-computed, finite volume flow equations. This way, a fully coupled, two-way FSI simulation can be performed to predict the thermoacoustic instabilities and the associated solid deformations in the burner. Overall, the predicted strongest pressure oscillation and wall displacement modes (frequency and amplitude) are all in good agreement with the experimental data across different operating conditions. The established workflow may support realistic gas turbine combustor design and prognosis.