Abstract: Applying the low-cost seismic isolation technology is a key way to reduce earthquake disasters of rural houses. Recently, the geotechnical seismic isolation (GSI) which uses low modulus materials between the structural foundation and the foundation soil has aroused widespread research interest. In this study, two low-cost GSI systems are proposed, which include the geotechnical seismic isolation system based on the sand cushion (GSI-SC) and the geotechnical seismic isolation system based on glass bead-sand cushion (GSI-GBSC). Through the large-scale shaking table model tests considering the site, the comparison tests between the single-layer masonry structure model with and without isolation system are carried out. The single-layer masonry structure model is made with a 1/4 scale. The north-south component of the El-Centro waves recorded in 1940 is selected as the input waves, and the peak input acceleration is 0.1g, 0.2g, and 0.4g, respectively. The results of the shaking table tests show that the two proposed low-cost GSI systems can decrease the seismic response of the structures and achieve the purpose of isolation. When the input acceleration amplitude is 0.4g, the GSI-SC system makes the reduction rate of the acceleration response of the structural roofs and the interlayer displacement response of the structures reach 33% and 39%, respectively, while the corresponding reduction rate of the GSI-GBSC system is 45% and 48%. Both the GSI-SC system and the GSI-GBSC system have strong isolation capability, simple construction and low cost, which are suitable for promotion in rural areas. In terms of isolation effect, the GSI-GBSC system has more superiority to the GSI-SC system.