In order to suppress the very directional vibration of a wind tunnel model sting system, the active vibration control method was proposed based on non-collocated configuration negative acceleration feedback (NAF) control algorithm. The very directional character of the lower-order modes was obtained by modal analysis, and the active wind tunnel model vibration control system with structural coupling embedded piezoelectric ceramic stack actuators was proposed. Based on the non-collocated configuration NAF control algorithm, the single-modal NAF control algorithm for the second-order mode and the dual-modal NAF control algorithm for the first two-order modes were proposed. The impact test shows that the dual-modal NAF control algorithm is more effective than the single-modal NAF control algorithm. Through the dual-modal NAF control algorithm, the damping ratio of the first two-order modes increases by nearly 13 times and 40 times respectively, and the setting time shortens by nearly 11s and 26s respectively.