The method of that isolation layer of prototype structure simplified to model structure in shaking table test was systematically researched based on equivalent principle, similarity theory, and considered three-dimensional seismic effect. Aimed at isolated structure in different aspect ratio, complete equivalent and part of equivalent simplified method were proposed. Equivalent of isolation layer, model's parameters of isolation bearings, coordinate certainty, similarity theory and so on were included in the method. the method was verified with shaking table tests of isolated structure with different aspect ratio, and combined with finite element numerical simulation, Theoretical derivation and numerical simulation were certified that the simplified method possessed well accuracy. And within the error allowed, the same dynamic characteristics of acceleration, velocity, displacement of isolation layer before simplification could be obtained. Therefore, the method could be used in shaking table test of model design.