Yunnan museum is in the high-intensity seismic area, and its structure form is complex, overrun and irregular steel reinforced concrete structure. It is significant for this kind of structure with special function to use seismic isolation technology. In order to confirm the vibration isolation effect and damage mechanism of museum isolation structure, shaking table tests of a scaled model (1:30) are accomplished. The dynamic characteristics of isolated bearing and fixed bearing model structure and seismic responses of model structure under fortification intensity and rare earthquake are tested and compared. Test results show that dynamic characteristics of isolation structure under different performance level earthquakes are stable, and vibration absorption effect is good. Horizontal peak accelerations of every storey of superstructure are less than that of table. Compared with non-isolated structure, acceleration responses of isolated structure are less. The drifts of every storey of superstructure meet requirements limit. Torsion responses of structure are small. The structure has no failure. Isolation bearings hysteretic curves are full and symmetric, and have no damage. Isolation technology can be applied into large, complex museum structure.