A novel control strategy was developed with an anode variable geometry ejector for a solid oxide fuel cell-gas turbine (SOFC-GT) system. The anode inlet temperature was controlled by combining two modes to achieve a greater controllable range: anode variable geometry ejector adjusting and after-burner fuel valve adjusting. Two tests were carried out under small-scale and large-scale load steps. The results indicate that all controlled variables can be effectively kept around set-point. Moreover, the critical parameters are kept within safe ranges, including steam-to-carbon ratio higher than 2.0, peak temperature gradient below 10 K/cm, peak time-dependent temperature gradient below 3 K/min, and surge margin higher than 15%. The developed novel control strategy can maintain almost constant SOFC spatial temperature. The spatial temperature variation is within 2.50 K under 5% load step, and within 14.30 K under 30% load step. Besides, the novel control strategy can keep the system efficiency at a high level (more than 63.21%) during the load tracking. Compared with the conventional control strategy with a fixed geometry ejector, the results demonstrated that the novel control strategy can significantly improve the system performance, especially the transient behaviors of after-burner fuel rate, turbine inlet temperature, and system efficiency.