A propulsion thrust control system and method for controlling thrust in a rocket motor includes configuring valves of an energized rocket motor to an initial total valve area according to a total thrust command. The total thrust command is converted into a commanded propellant mass flow discharge rate. A varying total valve area is computed from an error between the commanded propellant mass flow discharge rate and a calculated propellant mass flow discharge rate. The valves are reconfigured according to a distribution of the varying total valve area. The propulsion system includes a pressure vessel with valves and a controller for regulating the valve area according to a propellant mass flow discharge rate from the pressure vessel.