A Lyapunov-based adaptive controller using a command filtered approach is proposed for the nonlinear longitudinal. dynamics of an air-breathing reusable space vehicle (RSV). This paper also proposes the RSV's longitudinal dynamics including thrust misalignment, and the misalignment terms are considered as disturbances during the numerical simulation. The RSV's longitudinal dynamics are highly unstable due to model uncertainty and external disturbance. Model uncertainty includes the variation of aerodynamic coefficients, for which high fidelity modeling is not feasible in a hypersonic region. A minimized online parametric adaptation law using a tuning function is designed to compensate for the tracking errors by the variation of model uncertainties and external disturbance. A first-order constrained command filter is designed to handle the physical constraints of command signals and estimate the partial derivatives of stabilizing functions. Lyapunov-based stability analysis and numerical simulation results are presented to verify that the control and adaptation law can guarantee system stability and track a reference trajectory.