The uptake of non-EPI vaccines, such as influenza and pneumonia vaccines, are very low in China compared to other countries. In China, immunization services are provided by dedicated vaccination service providers (VSPs), and their recommendation is the key to improve vaccine uptake. This study explores VSP recommendation practices for non-EPI vaccines from a socio-ecological perspective. A mixed-methods study, combining a questionnaire survey and key informant interviews, was conducted in Anhui, Shaanxi, and Guangdong provinces. 555 VSPs completed the valid questionnaire, and 49 VSPs participated in in-depth interviews. Among the surveyed VSPs, 51.54% stated that they always or often recommended non-EPI vaccines in work, and the remaining half reported that they sometimes or never recommended non-EPI vaccines. Most VSPs interviewed communicated about non-EPI vaccines with the public in an informed style, not a presumptive one, and provided the public with all the decision-making latitude. The infrequent recommendation of non-EPI vaccines was widely prevalent among Chinese VSPs regardless of their individual characteristics, and was mainly driven by the interpersonal relationship, institutional arrangement, and public policy. Firstly, the VSPs were concerned about conflicts arising from the recommendation of self-paid vaccines and the risk of adverse reactions following vaccination. Secondly, high workloads left them insufficient time to communicate about non-EPI vaccines. Thirdly, there was no performance assessment or financial incentive for VSPs to recommend non-EPI vaccination, and their main responsibility was around EPI vaccination. Therefore, multi-level socio-ecological systems around non-EPI vaccination should be improved to optimize the communication between VSPs and the public, which include a better system of legal redress to resolve potential misunderstandings between the VSPs and the public, more effective workload management through whole-process health information system and strengthening public health workforce, and the introduction of performance assessment and appropriate incentives on non-EPI vaccination.