In China, many young and middle-aged rural residents move to urban areas each year. The rural elderly are left behind. The number of the rural left-behind elderly is increasing with urbanization, but it is unclear which indicators can be used to assess their health condition. The health risk assessment index system was developed to improve the health level of the rural left-behind elderly. A two-round web-based Delphi process was used to organize the recommendations from fifteen Chinese experts in geriatrics, health management, social psychology who participated in this study. Meaningfulness, importance, modifiability, and comprehensive value of the health risk assessment indicators in the index system were evaluated. The effective recovery rates of the two-round Delphi were 86.67% and 92.31%, respectively. The judgement coefficient and the authority coefficient were 0.87 and 0.82, respectively. The expert familiarity was 0.76. Ultimately, the health risk assessment index system for the rural left-behind elderly consisted of five first-level indicators, thirteen second-level indicators, and sixty-six third-level indicators. The final indicators can be used to evaluate the health of the rural left-behind elderly and provide the basis for additional health risk interventions.