BACKGROUND: This study aimed to assess the impact of the pandemic of the coronavirus disease 2019 (COVID-19) on neonatology residency training in a tertiary children's hospital in Chongqing, located in southwest China. Specifically, the study encompassed the effects on residents' education, lived experiences, well-being, and the quality of neonatal care delivered. As higher educational institutions adapt to the post-COVID-19 era after the pandemic disruption, it is imperative that educational designers/academics learn from their experiences and challenges in curriculum design and delivery, ensuring quality and relevance in education. METHODS: This study employed a mixed-methods approach to investigate the influence of the COVID-19 pandemic on neonatology residency training at a tertiary children's hospital in Chongqing. The first phase surveyed residents' perceptions and experiences of their clinical education and well-being during the crisis. The second phase compared the quality of neonatal care between the pre-pandemic and pandemic periods. RESULTS: The survey of 123 neonatology residents examines the effects of COVID-19 on their learning, training, and mental health. The survey showed that most residents adapted well to the situation. Still, some faced challenges in their clinical education and experiences, such as reduced clinical exposure and opportunities to see rare diseases and conditions. A retrospective analysis of clinical data revealed that 7,151 neonates were admitted to the neonatology department during the study period. There was a 27.6% decrease in neonatal admissions during COVID-19, with more premature births and transfers. Residents conducted fewer clinical procedures but managed more complex cases. During COVID, hospital stays and costs were higher, but antibiotic use was lower. Although the case-mix index (CMI) score increased during the pandemic (1.25 vs. 1.18, p < 0.05), there was no significant difference in the rates of readmission within 7 days or poor prognosis. CONCLUSIONS: Despite reduced clinical exposure, the quality of neonatal care was maintained through innovative training methods that enhanced comprehensive residency programs. The study suggested that neonatology residency education remained effective and resilient during the crisis. Exceptional health professional education is vital to train qualified physicians and enhance healthcare systems for future challenges.