The guidance and control system (GCS) is an important and indispensable component of hypersonic flight vehicle (HFV), and it can be viewed as a special cyber–physical system (CPS). However, the monitoring of the HFV dynamics is difficult since the inertial navigation equipment can only provides the information of acceleration and angular rate. In this case, the flexible states of HFV are difficult to be measured. This paper proposes a sliding mode observer (SMO) based GCS design method for HFV. With considering the measurement difficulties, the flexible states of HFV are assumed to be unmeasurable. Then a SMO is designed to estimated them. Combined with the actual flight environment of HFV, the measuring devices are assumed to be suffering from disturbance, then the SMO should not only guarantee the estimation error stable, but also reduce the influence of external disturbances. What is worse, the input of HFV is suffering from input delay, which brings more difficulties to the controller design. By state transformation,input delay model of HFV is transformed into a delay free model,then a SMO based robust controller is proposed for HFV based on the stable inversion controller design strategy. By the proposed SMO based controller, the GCS can be constructed for HFV. Numeral simulation are carried on HFV, and simulation results show shat, the designed SMO can realize the monitoring of flexible states of HFV and the designed GCS can get a good tracking performance.