Background <p>Compassion fatigue can lead to various physical and mental health issues and reduce the work efficiency and motivation of medical professionals. This study explored the prevalence of compassion fatigue among medical students and its relationship to their decision to continue working in clinical medicine after graduation from medical school.</p> Methods <p>A cross-sectional survey was conducted with clinical medicine students in several hospitals in Southwest China using convenience methods. The Chinese version of the Compassion Fatigue Scale was used to measure compassion fatigue. Additionally, the desire to have a career in clinical medicine after graduation was investigated to determine its relationship to compassion fatigue.</p> Results <p>A total of 473 medical students participated in the survey. Among the participants, 46 experienced mild compassion fatigue, 205 experienced moderate compassion fatigue, and 210 experienced severe compassion fatigue. The regression analysis showed that a night shift frequency of 2–3 times/week (odds ratio (OR) = 5.33, 95% confidence interval (CI) [1.35, 21.0]), working 8–10&#xa0;h per day (OR = 2.30, 95% CI [1.01, 5.22]), or working 10&#xa0;h per day or more (OR = 8.64, 95% CI [1.99, 37.6]) were factors of severe compassion fatigue. Furthermore, 158 participants reported that they did not often or always want to pursue a career in clinical work after graduation. Regression analysis revealed that low empathy satisfaction was an independent risk factor for students not wanting to continue in clinical practice post-graduation (odds ratio = 2.30, 95% CI [1.00, 5.31]).</p> Conclusion <p>Compassion fatigue is common among medical students and may significantly influence their intention to pursue a medical career after graduation. Educational institutions, medical facilities, and relevant departments should prioritize addressing compassion fatigue in medical students and implementing effective preventive and interventional strategies.</p>