Flood is common in China and causes extensive loss of property and human lives. Elderly is a vulnerable population prone to the detrimental impacts of floods. This survey aims to investigate the health status and the HRQoL of the elderly in Bazhong city after a major flood in 2011. A total of 1183 elderly (aged > 60) were surveyed through random sampling from eight villages in Bazhong city. Two-week healthcare-seeking rate and chronic diseases prevalence were recorded anonymously. Health-related quality of life (HRQoL) was measured by the Medical Outcomes Study Short Form-36 (MOS SF-36). Multivariate regression analysis was conducted to determine the associated factors of poor HRQoL. The two-week healthcare-seeking rate among post-flood Bazhong elderly was significantly higher than the references rate among rural elderly in Sichuan province (59.3% versus 55.7%, χ2 = 5.134, p = 0.013), but Bazhong elderly demonstrated a significantly lower prevalence of chronic disease (33.2% versus 44.4%, χ2 = 48.847, p < 0.001). All dimension scores among Bazhong elderly were significantly lower than the references scores in rural Sichuan elderly. The determinants of poor physical health included older age, singlehood, poor sleep patterns, and chronic diseases and so on. A marked decline in health status among elderly in Bazhong after the 2011 flood. Post-flood management targeting elderly need to be sensitive to their age, gender, married status and status of chronic diseases.