Supersonic blowdown wind tunnels provide controlled test environments for aerodynamic research on scaled models. During the experiments, the stagnation pressure in the test section is required to remain constant. Due to nonlinearity and distributed characteristics of the controlled system, a robust controller with effective flow control algorithms is required for this type of wind tunnels. In this paper, an extended Kalman filter (EKF) based flow control strategy is proposed and implemented. The control strategy is designed based on state estimation of the blowdown process under the EKF structure. One of the distinctive advantages of the proposed approach is its adaptability to a wide range of operating conditions for blowdown wind tunnels. Furthermore, it provides a systematic approach to tune the control parameters to ensure the stability of the controlled air flow. Experiments with different initial conditions and control targets have been conducted to test the applicability and performance of the designed controller. The results demonstrate that the controller and its strategies can effectively control the stagnation pressure in the test section and maintain the target pressure during the stable stage of the blowdown process.