Hypersonic vehicle with scramjet is a new kind of vehicle with bright future. With a study of its standard trajectories in half-velocity coordinate system, the fly velocity and design parameters were found to be the main factors to influence its skipping trajectories. The trajectory simulations in perturbation and standard atmosphere models showed that change of atmosphere parameters could influence the height, maximal load, maximal heat and total heat of trajectories. These factors should be considered while studying the vehicle design parameters, structure parameters, heat shield system and guide navigate and control (GN&C) system.