Present disclosure provides a test method and system for a seismic isolation structure, the method comprising: loading driving displacement time history signal into a substructure of the structure, recording restoring force time history feedback signal of the substructure; applying restoring force time history feedback signal to numerical substructure of seismic isolation structure, solving dynamic response of numerical substructure, recording structural displacement response time of the numerical substructure; calculating root-mean-square error (RMSE) of driving displacement time history signal and structural displacement response time signal; judging whether the RMSE is less than a threshold; if the RMSE is less than the threshold, ending the experiment; if the RMSE is not less than the threshold: correcting the time history signals according to a model identification algorithm, obtaining a corrected driving displacement time history signal of the next iteration, loading the corrected driving displacement time history signal onto the substructure, and repeating the steps.