The reasonability of the structure design of aircraft engine and after-body directly affects the components matching and performance of the engine. The numerical analysis for the internal and external field characteristics of the conformal asymmetric nozzle of flying-wing unmanned aerial vehicle in the typical flight condition was carried out by adopting the 3D Reynolds-averaged N-S equation and k-ωSST turbulence model. The thrust performance of afterbody nozzle and also the variation trend of the 3D flow characteristics against the blow-down ratio of secondary flow were obtained. The results show that under a fixed blow-down ratio of the engine nozzle, the main flow field characteristics of the after-body nozzle can be effectively improved by reasonably optimizing the secondary flow channel and increasing the blow-down ratio of secondary flow；when the flow rate of secondary flow and main flow is within the range of 0.2% to 1.86%, the changing range of nozzle axial thrust coefficient is about 3%. Overexpansion of the engine′s main flow is weakened to a certain extent and thrust loss of the engine is decreased. Therefore, the blow-down ratio of secondary flow has great influence on the performance of the after-body nozzle of unmanned aerial vehicle.