A direct control method is developed to control the spatial xenon oscillations in pressurized water reactors. The xenon and iodine concentration difference between the top and bottom halves of the core is estimated by using the extended Kalman filter (EKF), which is a closed-loop estimation method. The measurement equation used in the observer is the axial offset measurement equation, which reflects the xenon unbalanced effect on the axial offset. Meanwhile, some of the coefficients of the observer are estimated on-line to reduce estimation error resulting from model error, i.e., simplified xenon and iodine dynamics. Therefore, the estimation can be guaranteed to be accurate, and the success of the estimation does not greatly depend on the accuracy of the observer model. The predicted one-step ahead xenon concentration, by using the EKF, was used to calculate the possible axial offset variation, and then the control rod motion was calculated to compensate for it. The simulation results show that the proposed method successfully controls the xenon oscillations.