Rocket Assisted Take Off (RATO) technology is utilized for the takeoff phase of various types of UAVs. RATO creates heavy axial overload for a UAV system, which consequently increases the inlet pressure of the fuel pump of the UAV’s turbojet engine. This situation leads to an abrupt change in fuel supply for its combustor, eventually causing drastic changes in the operating state of the compressor system. In addition, it may potentially induce compressor surge. To resolve this problem, through an experimental investigation, this study delves into the dynamic response of the fuel system during the RATO phase. A two-zone dual-wave coupled compressor model has been established for the intake-turbojet engine system to scrutinize the aerodynamic stability of the turbojet engine during the RATO phase. The findings reveal that when the increase of fuel pump inlet pressure causes changes in the fuel flow rate, it is essential for the engine to re-establish aerodynamic equilibrium in order to mitigate the impacts of abrupt fuel flow step increases. Moreover, it has been observed that the more the ratio of the length of the intake and the cross-section area, the greater the contribution of the inertial force of airflow in the pipe it brings within the passage. This results in a stronger suppression of combustion chamber pressure and flow rate fluctuations induced by fuel step supply, thereby rendering the compressor less susceptible to surge. In summary, this research contributes valuable insights for appropriate matching of intakes, enhancing the ability of the turbojet engine against fuel step supply in the combustion chamber during the takeoff stage and augmenting the aerodynamic and thermodynamic overload resistance capability of the engine.