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Introduction Hypoxic-ischaemic encephalopathy (HIE), a leading cause of neurological disability in neonates, is managed with therapeutic hypothermia, yet systematic data on its aetiology and prognosis are lacking, particularly in China. Herein, our study addresses this gap by establishing a prospective registry in Shenzhen and aims to clinically characterise HIE, identify its risk factors and document its long-term outcomes.Methods and analysis We will recruit 200 neonates with HIE from 10 hospitals in Shenzhen, China, between January 2025 and December 2028. In parallel, clinical data will be collected during hospitalisation, with supplemental referral information obtained from birth hospitals via an online, specialised HIE database. We will include HIE severity, survival status and the incidence of serious complications, such as arrhythmias, pulmonary haemorrhage, neonatal acute respiratory distress syndrome, persistent pulmonary hypertension of the newborn and disseminated intravascular coagulation, to assess key outcomes of HIE in neonates.Longitudinal follow-up is scheduled for 18, 24 and 36 months, involving assessments using physical developmental scales, video-electroencephalogram (VEEG) recordings, the Chinese version of the Bayley Infant and Toddler Developmental Scale, Fourth Edition and cranial MRI at 18 months. The primary objectives of this study are to determine survival status, track loss-to-follow-up rates and evaluate neurodevelopmental outcomes at 3 years, with the ultimate goal of enhancing our understanding of HIE risk factors, hypothermia therapy and prognosis to reduce HIE-related morbidity and disability.Ethics and dissemination This study protocol has been approved by the Medical Ethics Committee of Shenzhen Children’s Hospital (Ethics No. 2024096), and the findings will be disseminated through presentations at national academic conferences and publication in peer-reviewed paediatric journals.Trial registration number ChiCTR2400094994.