Research of thrust asymmetry compensation control based on turbofan engine performance deterioration mitigating control (EPDMC) was conducted. An outer thrust loop based on nominal control system was investigated, which manipulates thrust indirectly and minimizes thrust asymmetry through setting expected thrust followed by twin engine. Then key technology including thrust setting, parameter estimation and speed command modification was introduced. Simulation performed under MATLAB/Simulink conditions indicates the feasibility of the thrust asymmetry compensation control system in automatic thrust synchronization.