Combustion instability is the biggest threat to the reliability of liquid rocket engines, whose prediction and suppression are of great significance for engineering applications. To predict the stability of a combustion chamber with a hypergolic propellant, this work used the method of decoupling unsteady combustion and acoustic system. The turbulence is described by the Reynolds-averaged Navier–Stokes technique, and the interaction of turbulence and chemistry interaction is described by the eddy-dissipation model. By extracting the flame transfer function of the combustion field, the eigenvalues of each acoustic mode were obtained by solving the Helmholtz equation, thereby predicting the combustion stability for the combustion chamber. By predictions of the combustion chamber instability with different flow rate distributions, it was found that the increasing of inlet flow rate amplitude will improve the stability or instability of combustion. The combustion stability of the chamber was optimized when the flow rate distribution for the oxidant was set more uniform in the radial direction. The heterogeneity of the flow rate distribution in the circumferential direction is not recommended, considering that a homogeneous flow rate distribution in the circumferential direction is beneficial to the combustion stability of the chamber.