A lower combustor inlet Mach number is desirable in order to design a compact, lightweight combustor and boost the overall performance of the scramjet engine. In this study, a thrust control strategy is proposed for a hydrogen-fueled scramjet taking into account the operating limitations, which is called the minimum combustor inlet Mach number rule since the combustor inlet Mach number is used as the control variable. By scheduling the fuel supply and modifying the intake geometry, the combustor inlet Mach number can be minimized while ensuring a certain thrust output within the operation constraints. In this manner, the scramjet engine can be operated with high specific thrust and low fuel consumption throughout the flight envelope. The thrust control strategy is further applied to a hydrogen-fueled scramjet in the hypersonic flight regime. Because the combustor inlet Mach number varies with flight conditions, the thrust strategy can be applied in practice by monitoring the following aerothermodynamic parameters in different flight regimes instead: (1) combustor outlet Mach number, (2) combustor inlet static temperature, and (3) combustor outlet static temperature. Furthermore, the effects of the thrust output on the division of flight regime are investigated, and the overall performance of the hydrogen-fueled scramjet engine obtained from applying the thrust control strategy is discussed in detail.