The flowfield inside a combustor of scramjet such as Hyshot II system is highly complicated and many factors have effect on its numerical prediction. Uncertainty and sensitivity analysis of aerodynamics prediction on Hyshot II intake configuration is performed in this work. The inflow conditions of intake configuration are of vital crucial since they directly determine the inflow conditions of combustor configuration, which in turn have a remarkable influence on the combustion and mixing process. Meanwhile, the varied flight conditions may also introduce great and direct impact on the performance in actual flight tests. It is significant to evaluate the uncertainties and sensitivities and to identify the critical factors of inflow conditions for the intake configuration. Five input parameters are selected as the epistemic uncertain variables. The flowfield prediction is conducted via using Reynolds-averaged Navier-Stokes simulations as the numerical study approach with standard Menter's shear stress transport turbulence model and species transport process for Hyshot II configuration. Stochastic expansions based on point collocation non-intrusive polynomial chaos, which require 42 deterministic simulations in this study, are employed to propagate and estimate the uncertainties. Meanwhile, Sobol indices are adopted to rank and indicate the individual contribution and to identify the critical inflow parameters. The results demonstrate that freestream Mach number and temperature are the dominated contributing parameters among the performance parameters. In addition, as observed from the wall-normal profile of related variables extracted at 355 mm in x coordinate direction in the simulation results, the freestream pressure plays a dominant role in determining the pressure distribution and the freestream temperature is the most prominent contributor to the distribution of temperature and velocity.