Background: Influenza is a major health threat to the elderly in China. Despite this, influenza vaccination rates still remain low and vary across regions that have different funding policies. In this study, we compare the vaccination status and influencing factors among older adults under the free, partial reimbursement, and self-paid vaccination strategies. Methods: Three cities with free, partial reimbursement, and self-paid influenza vaccination policies were selected. A cross-sectional, anonymous survey was then conducted. A total of 2265 elderly individuals aged 60 years and above were recruited using probability proportionate to size sampling. A standardized questionnaire was used during face-to-face interviews to collect data regarding the influenza vaccination status and influencing factors. The statistical analyses included chi-square tests, a multivariate logistic regression, and random forest models. Results: Among the 2265 participants (free policy region: n = 426; partial reimbursement region: n = 633; self-paid region: n = 1206), vaccination rates during the 2023–2024 season were significantly higher in the free policy region (53.29%) than in the partial reimbursement (20.85%) and self-paid (13.60%) regions (p < 0.001). The intention to vaccinate for the 2024–2025 season was also highest in the free policy region (68.78%), followed by partial reimbursement (47.71%) and self-paid (37.15%) regions (p < 0.001). This result demonstrated the same trend as the vaccination behavior. Cues to action (e.g., healthcare worker or family member recommendations) positively influenced vaccinations across all of the regions. In the self-paid region, perceived barriers, such as vaccine cost and side effect concerns, significantly reduced both behaviors and the next-season intention to vaccinate. Healthcare worker recommendations were key positive factors, while misconceptions and costs were major barriers to vaccination. Conclusions: Vaccination rates varied significantly across regions with different influenza vaccine subsidy policies. The free policy region demonstrated the highest coverage rate, while the self-paid region exhibited the lowest, suggesting that financial policies are a key determinant of vaccination uptake. Furthermore, free vaccination policies were associated with improved influenza vaccine knowledge among the elderly. Analysis of other influencing factors revealed that healthcare workers’ recommendations played a crucial role across all policy regions, though their impact on current-season vaccination behavior and next-season vaccination intention differed by subsidy context. Further studies are needed to explore the best approaches for optimizing region-specific subsidy strategies for promoting influenza vaccination among the elderly in China.