The control-structure interaction (CSI) between shaking table and eccentric load is one of the most important reasons causing the accuracy degradation of shaking table test. At present, the eccentric ratio (ER) of load and the coupling between actuators pose challenges to study the CSI. Thus, this paper establishes an analytical transfer function matrix of a shaking table and eccentric load. Based on the transfer function matrix, a comprehensive study is conducted to analyse the CSI effect under different eccentric ratio conditions. The analysis proves the influence of the CSI, and the CSI amplifies the actuator coupling more than 22 times at 20.00 Hz. Furthermore, a real-time CSI compensation strategy considering the actuator coupling is proposed. With the adopting of the proposed strategy, the coupling between two actuators is fully eliminated, and the correlation coefficients of ground motion records of two actuators are improved by 14.75% and 5.48%, respectively.