The growing demand for increasing the engine power of a liquid rocket is driving the development of high-power De-Laval nozzles, which is primarily achieved by increasing the expansion ratio. A high-expansion-ratio for De-Laval nozzles can cause flow separation, resulting in unsteady, asymmetric forces that can limit nozzle life. To enhance nozzle performance, various separation control methods have been proposed, but no methods have been fully implemented thus far due to the uncertainties associated with simulating flow phenomena. A numerical study of a high-area-ratio rocket engine is performed to analyze the aeroelastic performance of its structure under flow separation conditions. Based on numerical methodology, the flow inside a rocket nozzle (the VOLVO S1) is analyzed, and different separation patterns are comprehensively discussed, including both free shock separation (FSS) and restricted shock separation (RSS). Since the location of the flow separation point strongly depends on the turbulence model, both the single transport equation and two-transport-equation turbulence models are simulated, and the findings are compared with the experimental results. Therefore, the Spalart–Allmaras (SA) turbulence model is the ideal choice for this rocket nozzle geometry. A wavelet is used to analyze the amplitude frequencies from 0 to 100 Hz under various pressure fluctuation conditions. Based on a clear understanding of the flow field, an aeroelastic coupling method is carried out with loosely coupled computational fluid dynamics (CFD)/computational structural dynamics (CSD). Some insights into the aeroelasticity of the nozzle under separated flow conditions are obtained. The simulation results show the significant impact of the structural response on the inherent pressure pulsation characteristics resulting from flow separation.