Background <p>Moral decision-making in clinical nursing interns is a critical aspect of core nursing competencies. Empathy plays a dual role in moral decision-making, with both positive and negative influences. This study aimed to explore the impact of empathy on the moral decision-making of clinical nursing interns as well as other factors that influence their moral decision-making.</p> Methods <p>A cross-sectional study was conducted in July 2024 among 528 clinical nursing interns rotating through hospitals affiliated with six universities. Data were collected using a general information questionnaire, the Ethical Decision-Making Competence Scale (EDM-CS), and the Interpersonal Reactivity Index-C (IRI-C). Statistical analysis was performed using SPSS version 22.0.</p> Results <p>The level of empathy among clinical nursing interns was found to be moderately low. Notably, there was a weak correlation between empathy and the level of moral decision-making among the interns. Additionally, moral decision-making was associated with maintaining good relationships with mentors or patients during the internship period.</p> Conclusion <p>Strengthening ethical education and interpersonal communication skills before nursing students enter their clinical internship phase is crucial. Particular emphasis should be placed on shaping the personality traits of nursing students, appropriately maintaining their empathy, and finding a balanced distance between empathetic engagement and rational thinking.</p> Clinical trial number <p>Not applicable.</p>