The seismic resilience of water supply systems can be impacted by numerous factors, but what these factors are in the rural context of China is unknown. In this study, 41 potential influencing factors of seismic-resilience for rural water supply system (RWSS) were obtained through a literature review and semi-structured expert interview, comprising 26 general influencing factors (GFs) and 15 water supply safety influencing factors (SFs). This study verified and ranked these factors through a questionnaire survey delivered to RWSS stakeholders in Sichuan Province, China. Based on 123 valid, returned questionnaires, these factors are divided into 9 factor groups through factor analysis performed on GFs and SFs, respectively, of which “economic resilience” and “organizational resilience in disaster prevention stage” are shown to be the most important factor groups. Additionally, it found that the experience of earthquake events significantly affects the perceptions of stakeholders on the importance of certain factors. Specifically, stakeholders who have experienced an earthquake prioritize the post-earthquake resilience of the system, while those who have not experienced an earthquake prioritize the absorption capacity of the system in the disaster prevention stage. Thus, it is not appropriate to use fixed weights to evaluate the seismic resilience of RWSSs. Significantly, this outcome differs from existing findings on the resilience of Urban Water Supply Systems (UWSSs), where “technical resilience” is the key dimension. These findings can help decision-makers fully understand the factors affecting the seismic resilience of RWSSs in China, and in doing so, augment the strengthening of rural water supply.