In order to realize the wide frequency excitation and high accuracy control of a new type of large load-capacity seismic simulation shaking table (named large compound shaking table, LCST), it is necessary to study the in-depth mechanism, influence factors, and compensation algorithm of the LCST. In this paper, the mechanism model of LCST was established by transfer function matrix and the coupling characteristics were analyzed by Bristol method. Then, the three-variable control simulation analysis was carried out by Simulink. The specimen influence on the LCST was tested by setting different mass, frequencies, and damping ratios of the specimen. A series of simulation studies suggest that the control accuracy of LCST is most sensitive to the frequency of the specimen, and high natural frequency could even lead to system instability. For the sake of high-precision control, this paper proposed a feedforward decoupling compensation control (FDCC) strategy. Through numerical studies, the improved tracking of the FDCC strategy was demonstrated. In addition, the mature compensation methods in the conventional shaking table can be introduced reasonably into the control loop by FDCC strategy so that the LCST can more accurately replicate the characteristics of synthetic and historic earthquakes.