Neonatal necrotizing enterocolitis (NEC) is a devastating intestinal disease that primarily affects preterm infants. Unfortunately, no specific treatment for NEC is currently available, making it crucial to further investigate its underlying mechanisms. In this study, we aimed to identify the key target gene, CHI3L1, which was significantly upregulated in the intestinal tissues of both affected children and model mice from the GEO database. CHI3L1 is known to play important roles in inflammatory and immune responses, as well as in tissue damage and repair, all of which are closely associated with the development of NEC. We conducted validations at both the cellular and animal levels, demonstrating that the inhibition or knockdown of CHI3L1 significantly reduced the severity of NEC. Mechanistic investigations revealed that the knockdown of CHI3L1 inhibited the PI3K-Akt-FoxO1 signalling pathway, alleviating excessive autophagy in intestinal epithelial cells and subsequently reducing injury and inflammatory responses. Clinical studies have revealed that elevated serum CHI3L1 expression in paediatric patients is associated with both the occurrence and severity of necrotising enterocolitis NEC, demonstrating positive correlations with the Duke Abdominal Assessment Scale (DAAS), C-reactive protein (CRP), procalcitonin (PCT), red cell distribution width (RDW), and lactate dehydrogenase (LDH) levels. In conclusion, our findings confirmed a close relationship between CHI3L1 and the occurrence and severity of NEC, suggesting that it may mitigate inflammatory responses and tissue damage by alleviating excessive autophagy in intestinal epithelial cells. Therefore, targeting CHI3L1 may be an effective strategy to combat NEC.