The traditional self-built houses with a bottom frame structure, still prevalent in rural areas, pose a significant risk of damage during earthquakes due to the structural weaknesses of the first and second floors. Despite this vulnerability, many residents continue to construct such houses due to their structural convenience. This study focuses on a rural self-built house with a frame bottom layer and three masonry upper layers. By subjecting the structure to seven seismic waves, we analyze the seismic responses of traditional seismic structures, bottom shear wall structures, foundation isolation structures, and storey separation structures. A comparative assessment of the seismic performance of these four structures under earthquake conditions is conducted. The study confirms the advantages and feasibility of implementing base shear wall and isolation technologies in rural self-built bottom frame structures. The findings reveal that bottom shear walls can mitigate seismic damage to some extent. Additionally, the implementation of isolation technology can effectively extend the structure's period and prevent site-specific vulnerabilities. When foundation isolation is applied, structural acceleration, interstory shear, interstory displacement, and base shear can be reduced from 18.261–32.098% of those observed in traditional seismic structures, indicating a significant improvement in seismic resilience. Moreover, the seismic performance of storey separation surpasses that of bottom shear walls, while foundation isolation outperforms both storey separation and bottom shear walls in terms of seismic performance.