Background: The disease burden of seasonal influenza is substantial in China, while there is still a lack of nationwide economic burden estimates. This study aims to examine influenza-like illness (ILI) prevalence, healthcare-seeking behaviors, economic impact of ILI, and its influencing factors among three priority groups during the 2018–19 influenza season. Methods: From August to October 2019, 6668 children’s caregivers, 1735 chronic disease patients, and 3849 elderly people were recruited from 10 provinces in China to participate in an on-site survey. The economic burden of ILI consisted of direct (medical or non-medical) and indirect burdens, and a two-part model was adopted to predict the influencing factors of total economic burden. Results: There were 45.73% children, 16.77% chronic disease patients, and 12.70% elderly people reporting ILI, and most participants chose outpatient service or over-the-counter (OTC) medication after ILI. The average economic burden was CNY 1647 (USD 237.2) for children, CNY 951 (USD 136.9) for chronic disease patients, and CNY 1796 (USD 258.6) for the elderly. Two-part regression showed that age, gender, whether the only child in the family, region, and household income were important predictors of ILI economic burden among children, while age, region, place of residence, basic health insurance, and household income were significant predictors of ILI economic burden among chronic disease patients and the elderly. Conclusions: A large economic burden of ILI was highlighted, especially among the elderly with less income and larger medical burdens, as well as children, with higher prevalence and higher self-payment ratio. It is important to adopt targeted interventions for high-risk groups, and this study can help national-level decision-making on the introduction of influenza vaccination as a public health project.