Objective To investigate the application effect of a virtual simulation teaching system based on DeepSeek technology in the clinical training of neonatal resuscitation. Methods A total of 48 clinical medicine (“5+3” integrated program) students from the 2020 cohort, interning in the Department of Neonatology of the First Affiliated Hospital of Harbin Medical University between January and June 2025, were selected and randomly divided into a trial group (n=24) and a control group (n=24). The trial group received training using a virtual simulation teaching system integrated with DeepSeek technology, featuring dynamic physiological response, natural language interaction, and hierarchical intelligent feedback. The control group received traditional virtual simulation teaching. After 6 hours of teaching, outcomes were evaluated through theoretical assessments, objective structured clinical examination (OSCE), key decision-making accuracy, and teaching satisfaction questionnaires. Results The theoretical score (93.5±3.3 vs. 84.7±4.9), OSCE score (95.3±2.6 vs. 86.1±4.3), and key decision-making accuracy [(91.6±3.7)% vs. (77.3±6.4)%] of the trial group were significantly higher than those of the control group (P<0.001). The trial group outperformed the control group in all OSCE subdomain scores (rapid assessment and initial resuscitation: 24.1±1.0 vs. 21.3±2.2; positive pressure ventilation: 23.8±1.2 vs. 20.1±2.1; chest compressions: 18.9±1.1 vs. 16.2±1.8; drug therapy: 14.3±0.9 vs. 12.0±1.5; teamwork and communication: 14.2±0.8 vs. 11.5±1.6) and in the accuracy rates for all key decision points [whether to initiate initial resuscitation: (93.8±4.5)% vs. (82.1±8.7)%; whether to initiate positive pressure ventilation: (92.9±5.3)% vs. (79.6±10.2)%; whether to correct ventilation: (90.4±6.1)% vs. (75.0±11.5)%; whether to initiate chest compressions (94.2±5.1)% vs. (70.8±12.3)%; whether to use epinephrine: (92.5±6.2)% vs. (68.3±14.1)%], with all differences being statistically significant (P<0.001). The teaching satisfaction survey showed that the satisfaction rates in the trial group for the dimensions of immersion (95.8% vs. 54.2%), knowledge understanding (91.7% vs. 58.3%), skill improvement (91.7% vs. 62.5%), decision-making logic (95.8% vs. 50.0%), feedback effectiveness (95.8% vs. 41.7%), and learning confidence (91.7% vs. 45.8%) were all significantly higher than those in the control group (P<0.05). Conclusion The DeepSeek-based virtual simulation teaching system can effectively enhance the quality of neonatal resuscitation training, significantly improving students’ clinical decision-making abilities, operational skills, and teamwork competence, demonstrating good application prospects in medical education.