Objective The reference range for perfusion index （PI） in healthy newborns was established， and the prognostic value of PI at multiple time points （6 h， 18 h， 24 h， 48 h， and 72 h） in critically ill newborns was evaluated. Methods A total of 100 healthy neonates born at the Hainan Women and Children's Medical Center between July 2022 and September 2024， along with 142 critically ill neonates admitted to the neonatal intensive care unit， were enrolled as study participants. The healthy neonates constituted the control group， while the critically ill neonates were categorized into low-risk （n = 44）， medium-risk （n = 61）， and high-risk （n = 37） groups according to disease severity. The clinical outcomes of the critically ill neonates were recorded and classified into poor prognosis （n = 38） and good prognosis （n = 104） groups. PI values were monitored in all neonates from 6 to 72 hours after birth. Spearman correlation analysis was performed to assess the association between illness severity and PI values during this period， while logistic regression analysis was employed to examine the relationship between PI values and prognosis in critically ill neonates. Receiver operating characteristic （ROC） curve analysis was conducted to evaluate the predictive value of PI for poor prognosis， and the optimal cutoff threshold for prognosis prediction was determined. Results The PI values of healthy neonates between 6 and 72 hours after birth ranged from 2.61 to 3.31. Critically ill neonates exhibited consistently lower PI values than their healthy counterparts during the same period， with statistically significant differences observed across neonates of varying illness severity （P < 0.05）. PI values in all groups gradually increased within the first 72 hours post-birth （P < 0.05）. Neonatal illness severity was negatively correlated with PI values measured at 6， 18， 24， 48， and 72 hours after birth （P < 0.05）. Furthermore， neonates in the poor prognosis group had significantly lower PI values between 6 and 72 hours compared to those in the good prognosis group （P < 0.05）. Reduced PI values were significantly associated with an increased risk of poor prognosis in critically ill neonates （P < 0.05）. The predictive performance of PI values for poor prognosis， as assessed by the area under the curve （AUC）， yielded values of 0.760， 0.779， 0.768， 0.797， and 0.808 at 6， 18， 24， 48， and 72 hours， respectively， with corresponding cut-off values of 0.88， 1.12， 1.25， 1.65， and 1.82. Conclusion The PI values measured between 6 and 72 hours after birth are closely associated with disease severity in neonates， with lower PI values indicating a poorer prognosis. These early postnatal PI measurements demonstrate auxiliary predictive value for the outcomes of critically ill neonates.