Symmetry breaking occurring in annular combustors shows different stability patterns due to the formation of nondegenerate modes with different frequencies. This also brings about more profound complexity for control methodology. This paper presents a three-dimensional analytical model to investigate how to control nondegenerate azimuthal modes by modifying the wall boundary conditions of a multiburner annular combustor. The stability of the system can be evaluated by solving the eigenvalue of the dispersion relation equation derived in this study. Results show that changes in the parameters of the perforated liner cause different performance in nondegenerate modes due to frequency splitting. Meanwhile, the asymmetric perforated liner alters the original asymmetry of the annular combustor, inducing a shift in the nature of nondegenerate modes when significant symmetry breaking exists. Furthermore, variations of pressure amplitude in the backing cavity lead to diverse acoustic energy dissipation and even distinct stability patterns under two types of azimuthally nonuniformly perforated liner. Overall, this paper presents a new methodology for suppressing nondegenerate azimuthal modes under symmetry breaking by utilizing a perforated liner in an annular combustor. Additionally, a clear understanding of the evolution behavior of nondegenerate modes is also provided by studying their stability behavior and energy dissipation.