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Background: Education is an important part of the work of most doctors. Clinical preceptors act as role models and supervisors. Preceptors' quality of supervision strongly influences the learning quality of clinical interns (Bartlett et al. BMC Med Educ 20:165, 2020). To ensure a consistent approach to every preceptorship experience, the competency of clinical preceptors should be assessed to ensure that the desired outcomes are achieved. This study aims to evaluate clinical preceptors' competency in learner-centered teaching, to provide constructive feedback to develop the preceptors' competency and improve supervisory skills and internship quality at Kunming Medical University (KMU) in Kunming of China. Methods: This is a cross-sectional study with a quantitative self-administered online questionnaire. The convenience sampling technique was employed. In the undergraduate internship stage of KMU, clinical preceptors (N = 340) and interns (N = 487) were invited to use the augmented Stanford Faculty Development Program questionnaire (SFDPQ) (Stalmeijer et al. Med Teach 30:e272–e277, 2008), to (self-) assess the preceptor's competency of learner-centered teaching on a five-point scale (1 = strongly disagree, 5 = strongly agree). Results: Two hundred twenty-eight preceptors and two hundred thirty-six interns completed the questionnaire correctly. Overall, the assessment was positive, but the preceptors' self-assessment significantly higher than the interns' (p < 0.00). The overall mean of each category of preceptors' self-assessment was greater than 4.5, with no difference based on educational qualification. Male preceptors scored significantly higher in two categories than female preceptors. Preceptors under 30 years of age with less than 5 years of teaching experience rated "Teacher's knowledge and attitude" lower than those over 40 years of age with more than 5 years of experience (p < 0.05). There were statistically significant differences in the four categories across disciplines (p < 0.05). Undergraduate interns rated "Teachers' knowledge" as the highest category and "Learning climate" as the lowest, and interns of different genders are evaluated without distinction in all categories of SFDPQ. Conclusions: Employing the augmented SFDPQ to evaluate learner-centered teaching competency of clinical preceptors, offers potentially useful information for delivering constructive feedback. Combining self-evaluations with learner evaluation data can contribute to exploring preceptor competency development framework to guide them in targeted learner-centered teaching skill and acquisition and improvement, finally improving the overall quality of internships. [ABSTRACT FROM AUTHOR]