Objective To analyze the relationship between the perception of the medical education environment based on pediatric blended learning and students' autonomy in learning. Methods The clinical medicine students from the First Clinical School of Wuhan University who had completed the blended learning courses in pediatrics were enrolled as participants. The Dundee ready education environment measure (DREEM) scale and the autonomy in learning rating scale for college students were adopted to investigate the perception of the medical education environment and autonomy in learning. Results The perception of the medical education environment among the clinical medicine students was generally positive. The order of score rating among dimensions was as follows: perception of teachers ＞ perception of learning ＞ perception of academic atmosphere ＞ perception of environment ＞ social and self-perception. The scores for self-regulation, learning strategies, content and environment, learning motivation, and overall autonomy in learning were 67.85%, 72.86%, 65.56%, 70.63%, and 68.97%, respectively. The result of the correlation analysis revealed that the scores of the internal dimensions of both the DREEM scale and the Autonomy in Learning Rating Scale for college students were significantly positively correlated with their own total scores (P＜0.05). Moreover, there were significant positive correlations observed among the scores of different dimensions within each scale (P＜0.05). Additionally, the scores of each dimension and the total score of the Autonomy in Learning Rating Scale for college students were significantly positively correlated with the scores of different dimensions and the total score of the DREEM scale (P＜0.05). Conclusion Clinical medicine students who experienced pediatric blended learning had a generally positive perception of the medical education environment, and their autonomy in learning was good and closely related to their perception of the medical education environment. In the implementation of blended learning, continuous optimization of teaching content, improvement of the teaching proficiency of teachers, and proactive enhancement of the medical education environment will help enhance clinical medicine students' satisfaction with the educational environment, as well as their learning interest and autonomy in learning, thus promoting the sustainable development of medical education reforms more effectively.