Simulated altitude test is an essential exploring, debugging, verification and validation means during the development of aero-engine. Free-jet engine test can simulate actual working conditions of aero-engine more realistically than direct-connect engine test but with relatively lower cost compared to propulsion wind tunnel test, thus becoming an important developing area of simulated altitude test technology. The Flight Conditions Simulating Control System (FCSCS) is of great importance to the Altitude Test Facility (ATF) but the development of that is a huge challenge. Aiming at improving the design efficiency and reducing risks during the development of FCSCS for ATFs, a Hardware-in-the-Loop (HIL) simulation system was designed and the mathematical models of key components such as the pressure stabilizing chamber, free-jet nozzle, control valve and aero-engine were built in this paper. Moreover, some HIL simulation experiments were carried out. The results show that the HIL simulation system designed and established in this paper is reasonable and effective, which can be used to adjust control parameters conveniently and assess the software and hardware in the control system immediately.