Objective To analyze the protective effect of amygdalin against necrotizing enterocolitis (NEC) in neonatal rats. Methods 60 healthy 7-day old SD rats were divided into control, model and low-dose, middle-dose and high-dose amygdalin groups, and salazosulfadimidine group by a random number table with 10 rats in each group. Except for the control group, hypoxic cold stress combined with formula milk for invasive feeding was applied to establish NEC models in the other groups. The low-dose, middle-dose and high-dose amygdalin groups were administered with 20, 40 and 80 mg / kg amygdalin, respectively, whereas the salazosulfadimidine group was administered with 300 mg / kg salazosulfadimidine for 5 days. At 12 h after the last treatment, changes in weight were recorded. HE staining of ileocecal tissues was conducted. Ileocecal tissue damage was scored by intestinal damage criteria. The apoptosis rate was determined by TUNEL staining. The serum levels of inflammatory factors ( tumor necrosis factor α (TNF-α), interleukin-6 ( IL-6), interleukin-1β (IL-1β), superoxide dismutase (SOD), malondialdehyde (MDA) and glutathione peroxidase (GSH-Px)) were measured by enzyme-linked immunosorbent assays. The expression levels of NOD-like receptor protein 3 (NLRP3), apoptosis-associated speck-like protein containing a CARD (ASC) and cysteine aspartase (Caspase-1) were measured by Western blot. Results Compared with the control group, the weight of rats was significantly decreased in the model group, while the intestinal damage score, apoptosis rate of intestinal tissues, TNF-α, IL-6, IL-1β, SOD, MDA and GSH-Px levels, and expression levels of NLRP3, ASC and Caspase-1 were increased significantly (P<0.05). Compared with the model group, the weight of rats was significantly increased in middle-dose and high-dose amygdalin groups, and the salazosulfadimidine group, while the intestinal damage score, apoptosis rate of intestinal tissues, TNF-α, IL-6, IL-1β, SOD, MDA and GSH-Px levels, and expression levels of NLRP3, ASC and Caspase-1 were decreased significantly (P< 0. 05). Conclusions Amygdalin has a protective effect against NEC in neonatal rats, which effectively reduces intestinal tissue damage, relieves the inflammatory response and oxidative stress, and reduces the apoptosis rate in intestinal tissues. However, the specific mechanism is unclear, which requires further clinical exploration.