The medical learning environment (MLE) exerted a profound influence on students' physical, psychological, and professional development. University prestige and ranking significantly shape students' self-perception and self-esteem. Nevertheless, the relationship between university category and MLE perception remained unexplored. Our study collected 10,901 questionnaires from 12 universities, spanning six categories. John Hopkins Learning Environment Scale (JHLES) was administrated to assess MLE perceptions. Utilizing a cross-sectional design, we categorized participants into high or low JHLES groups. Next, we conducted Chi-square and parametric or non-parametric tests to analyze the relationship between perception of MLE and university category. Subsequently, we performed a multivariate logistic regression and developed a nomogram to predict the likelihood of low JHLES scores. And the model performance was assessed through receiver operating characteristic (ROC) curves, decision curve analysis (DCA), and calibration curves. Our study revealed a significant association between university category and MLE perception. Specifically, students from top-tier universities were prone to negative MLE perceptions. Through multivariate logistic regression analysis, we validated university category as an influencing factor ( < 0.001). Moreover, our nomogram demonstrated reliability and consistency in predicting students' MLE perspectives. The university category emerged as a predictor for perception of MLE. Students from prestigious institutions manifested an increased likelihood of negative MLE perceptions.