Hypersonic vehicles have complex structures with multiple sources of uncertainties, and the presence of uncertainties may lead to the vehicles’ structural failure. Aiming to ensure the flight safety and structural reliability of a hypersonic vehicle, this study proposes a vibration optimization control method based on non-probabilistic time-dependent reliability. Due to the complex structure of the vehicle, its forebody and aftbody are modeled as two cantilever beams with the center of mass of the vehicle as the fixed fulcrum, respectively, and a vibration control model of cantilever is derived. Considering that the uncertainties in practical engineering are not easy to be counted, the uncertain parameters are quantified by using interval variables, and the dynamic response and time-dependent reliability of the uncertain system are analyzed based on the subinterval method and the non-probabilistic time-dependent reliability analysis method (NTRAM) designed in this paper. Further, to ensure the high reliability of the vehicle, an optimal robust linear quadratic regulator (ORLQR) method with the constraint of time-dependent reliability is proposed. The analysis of the numerical examples shows that the parameter uncertainty has a certain effect on the reliability of the vehicle, and verifies that the proposed ORLQR method can effectively control the vibration and slow down the reliability decline.