The objective of this paper is to investigate the uncertainty in the bondline temperature response of a flexible thermal protection system subject to uncertain parameters in the hypersonic flowfield and thermal response modeling of a Hypersonic Inflatable Aerodynamic Decelerator configuration for ballistic Mars entry. An inflatable decelerator with 10m major diameter is selected for this study based on the forebody dimensions scaled from the 6m test article that was tested in the NASA Ames National Full-Scale Aerodynamics Complex facility. A global nonlinear sensitivity analysis study for the bondline temperature uncertainty showed that the dimension of uncertain parameters can reduced from 22 to eight. Uncertainty analysis of the bondline temperature in the reduced dimensions indicated that the bondline temperature varies by as much as 125% above the nominal prediction and exceeds the temperature limit of 400oC. The largest uncertainty occurred at 70 seconds in the trajectory prior to separation of the inflatable decelerator for transition to a secondary descent technology. The main contributors to the bondline temperature uncertainty were the insulator and outer fabric conductivities and the freestream density. The thickness and initial density of the insulator layer, closest to the gas barrier layer, was also shown to be a significant contributor to the bondline temperature uncertainty, especially earlier in the trajectory.