This article presented simulation and control of a liquid oxygen/liquid methane variable thrust rocket engine pressurized by the electric pump in the throttling process. To get a proper injection pressure drop, the variation of the injection area was investigated and determined. In the control scheme, the combustion pressure and mixture ratio were the targets. To simplify the control scheme, the pressure and mixture ratio were correlated to the oxygen mass flow rate and methane mass flow rate, respectively. By controlling the propellant mass flow rate, the target engine thrust was reached. In addition, the influence of mass flow rate measurement points on the control effect was analyzed. The simulation results showed that the designed controller can reduce the overshoot of the critical engine parameters. Therefore, the maximum temperature of the thrust chamber wall after the regenerative cooling was decreased. Consequently, the thrust control errors were within 3% except for the points where the thrust changed suddenly, which can meet the mission requirements.