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Background With the continuous development of the training program of rural order-oriented medical students (referred to as publicly-funded medical students) in China, the talent team of general practice is constantly enriched, and the professional identity status and its influencing factors in rural order-oriented medical students have become the focus of current attention. Objective To analyze the influencing factors of professional identity in rural order-oriented medical students. Methods Purposive sampling method was used to interview the 30 rural order-oriented medical students from 2018 to 2022 grade of Traditional Chinese Medicine (five-year system) Beneficiary Class of Shandong University of Traditional Chinese Medicine by semi-structured interviews from December 2022 to March 2023. The interview data were coded and analyzed by using open coding, axial coding, and selective coding, following the Anselm Strauss and Juliet Corbin programmatic grounded theory approach. Results A total of 482 initial concepts and 47 basic categories were extracted by open coding, 9 main categories obtained by axial coding. A typical relationship structure was formed by selective coding, and it showed that the influencing factors of professional identity in rural order-oriented medical students were consisted with six dimensions of career cognition, career behavior, career choice, career will, career emotion, and career belief. Conclusion The influencing factors of professional identity in rural order-oriented medical students are composed of six dimensions, including career cognition, career behavior, career choice, career will, career emotion, and career belief, of which career cognition, career behavior, and career choice belong to the exogenous factors, while career will, career belief, and career emotion belong to the implicit factors.