To observe the practical effect of the multidisciplinary collaborative diagnosis and treatment management system for the neonatal brain injury (NBI). Methods: The hospital started to use the multidisciplinary collaborative diagnosis and treatment (MDT) management system for NBI from January 2022. 159 neonates without MDT who had admitted to the hospital from January to December 2021 were included in control group, and 228 neonates with MDT who had admitted to the hospital from January to December 2022 were included in observation group. The scores of Neonatal Behavioral Neurological Assessment (NBNA) and the Bayley Scales of Infant and Toddler Development (BSID), the time to symptom relief, the duration of hospital stay, the complications rate and the clinical efficacy of the neonates before and after treatment were compared between the two groups. Results: After treatment, the total effective rate (95.6%) of the neonates in the observation group was significantly higher than that (89.9%) of the neonates in the control group. The scores of NBNA primitive reflex (5.16±0.68 points), the general reaction (5.02±0.63 points), the active muscle tension (6.83±0.92 points), the behavioral ability (10.12±1.76 points), the passive muscle tension (6.95±0.94 points), the BSID motor development index (104.17±10.75 points) and the mental development index (96.12±9.85 points) of the neonates in the observation group were significantly higher than those (4.29±0.75 points, 4.48±0.71 points, 5.14±0.83 points, 8.65±1.32 points, 5.23±0.87 points, 91.32±10.06 points and 84.35±8.62 points) of the neonates in the control group. The relief time of scalp hematoma (5.73±1.02d), pale face (5.90±1.13d) and tension of fontanelle (4.85±0.84d), and the hospitalization time (11.05±2.73d) of the neonates in the observation group were significantly shorter than those (6.12±1.05d, 6.34±1.08d, 5.72±1.26d, and 12.96±3.14d) of the neonates in the control group. The total incidence of complications (4.8%) of the neonates in the observation group was significantly lower than that (18.9%) of the neonates in the control group (all P<0.05). Conclusion: The MDT management system for NBI of the neonates can promote their symptom relief, shorten their hospital stay, reduce their risk of complications, and improve their clinical efficacy.