The sensor-based incremental nonlinear dynamic inversion (INDI) using angular acceleration measured by inertial measurement unit (IMU) sensor is a very robust control method on various model uncertainties when the aircraft maneuvers with moderate angle-of-attack (AoA) and high gravity in transonic speed flight conditions. However, the measured angular acceleration has time delay characteristics due to actuator and aircraft dynamics, IMU sensor dynamics, differential angular rate and structural coupling filter (SCF) and so on. These characteristics of angular acceleration feedback reduce dramatically the stability margin of the control system. In this paper, we propose the synchronization filter design method of the control surface feedback path for improving stability margin, based on the proposed hybrid INDI control method using error between the angular acceleration measured from IMU sensor and the angular acceleration calculated from on-board model (OBM) and control surface feedback. To evaluate the proposed control method, we perform the frequency-domain linear analysis and the time-domain simulation. As a result of the evaluation, synchronization method of control surface feedback not only improves the stability margin characteristics of the control system but also eliminates the structural coupling in low frequency range by designing the control surface command feedback using actuator command which is the output of flight control computer (FLCC).