A flying characteristic simulation method is studied for two-stage turbocharging Compression Ignition engine propeller propulsion system, intended for medium/high altitude low-speed long-endurance multi-role UAV systems at 10 ∼ 20 kilometers high, with cruising speed 100 ∼ 250 km/h. Introducing the simulation method for gas turbine engine with component models, based upon component maps or algebraic equations, this method solves joint-working equations of the propulsion system by Newton iteration method to obtain cooperation points of the system. A full-power holding requirement and turbocharger-engine collaboration condition are stated. The regulating rules in both full-power holding mode and power lapse mode are analyzed. The influences of regulating rules on turbocharger operating lines are placed. Finally, the altitude-velocity characteristics of the propulsion system and components are investigated. The research shows three results. This method converges rapidly that usually it needs only 5–6 iterations to obtain one operating point. The regulation scheme of two gas-bypass valves can not only meet the design objectives, but also allow an effective adjusting to the operating points of the turbochargers. This method can be extended conveniently to the simulations of more complex multi-stage turbocharging systems.