The aim of the present study was to investigate the impacts of n-3 PUFA and lymph drainage (D) on intestinal ischaemia–reperfusion (I/R) injury in rats. A total of forty-eight Sprague–Dawley male rats were randomly divided into three groups (n 16): normal diet (N), enteral nutrition (EN) and EN plus n-3 PUFA. Each group was further divided into lymph drainage (I/R+D) and non-drainage (I/R) sub-groups (n 8). After 5 d with different nutrition regimens, the rats were subjected to 60 min ischaemia by clamping the superior mesenteric artery, followed by 120 min reperfusion. At the same time, the rats in the I/R+D sub-groups were treated with intestinal lymph drainage for 180 min. Organs were harvested and we detected the cytokine, endotoxin, and expression of Toll-like receptor (TLR) 4 mRNA and its endogenous ligand high-mobility group box 1 (HMGB1). We found that the serum levels of HMGB1, inflammatory cytokine and endotoxin in the three I/R+D sub-groups were significantly lower than those in the N (I/R) and EN (I/R) sub-groups (P < 0·05). The activation of NF-κB and the expression of HMGB1 and TLR4 mRNA significantly increased in the jejunum, ileum, liver and lung after intestinal I/R injury, but notably lower in the I/R+D groups than those in I/R (P < 0·05). The injury degree and HMGB1 expression were decreased in the n-3 PUFA group than in the N and EN groups. We preliminarily concluded that nutrition with n-3 PUFA and/or intestinal lymph drainage may reduce HMGB1 and inflammatory cytokine in serum and lymph and inhibit the expression and signal transmission of TLR4 mRNA, thereby alleviating intestinal I/R injury in rats.