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Background Neonatal hypothermia, especially occurring in the early postnatal period, is a critical condition associated with increased morbidity and mortality. Effective thermal management is essential, yet regional data on early postnatal hypothermia (EPH) incidence among critically ill neonates requiring inter-hospital transport are limited.Methods This retrospective, multicentre, observational cohort study involved critically ill newborns transported from six delivery hospitals, including two women’s hospitals and four general hospitals, to a tertiary care neonatal centre between January 2022 and April 2023. According to the lowest body temperature measured within the first postnatal 2 hours, patients were divided into four groups: normal group (36.5°C–37.5°C), mild EPH group (36.0°C–36.4°C), moderate EPH group (32.0°C–35.9°C) and severe EPH group (<32°C). The perinatal risk factors and early outcomes within 7 days after birth (including mortality, hypoglycaemia, pulmonary haemorrhage and shock) were analysed.Results A total of 457 newborns were enrolled and 82.1% experienced EPH, including 42.5% mild, 39.6% moderate and 0% severe. Notably, the incidence of EPH was significantly higher in very preterm infants (VPIs), reaching 93.2%. Based on multivariable analysis, general hospital births (OR 5.00; 95% CI 3.20 to 7.88) and delivery room intubation (OR 1.74; 95% CI 1.19 to 2.55) increased the risk of hypothermia severity (p<0.05). Women’s hospitals demonstrate superior adherence to neonatal thermoregulation protocols compared with general hospitals. Mortality and other early complications during postnatal 7 days showed no significant differences among groups.Conclusion EPH remains common among critically ill transported neonates, particularly in VPIs. Variations in thermal management practices, especially in general hospitals, may contribute to its occurrence. These findings underscore the need to establish and implement standardised, targeted temperature management protocols across delivery settings to improve neonatal care quality.