Findings of previous studies have revealed that intestinal mucosal mast cells (IMMCs) are involved in small intestinal ischemia‑reperfusion injury (IIRI). However, time-course changes of mast cell counts and mast cell function in this process remain unclear. The present study aimed to observe the number of IMMCs and to investigate the correlation between their activation and small intestine injury at various time points during the period of small intestinal ischemia reperfusion (IIR). Healthy male Kunming mice were randomly divided into five groups, and were subjected to occlusion of the superior mesenteric artery (SMA) for 30 min and followed by reperfusion for 1, 3, 6 and 12 h. By contrast, the SMA was isolated but not clamped in the baseline group. Chiu's scores were assessed by light microscopy, tryptase protein and MCP7 protein expression in the intestine were quantified, and mast cell counts and levels of histamine and TNF-α in the intestine were measured. The results showed that IIR induced severe intestine injury within 12 h as demonstrated by Chiu's scores that was greatly increased as compared to the baseline group, accompanied by increased mast cell counts, histamine and TNF-α levels. However, the Chiu's scores were reduced in the IIR 12 h group compared with the IIR 1 h, IIR 3 h and IIR 6 h groups, with concomitant decreased mast cell counts, histamine and TNF-α levels. The tryptase and MCP7 protein expression was markedly increased in the IIR 1 h and IIR 3 h groups as compared with the baseline group, whereas this expression was gradually decreased at 6 and 12 h after reperfusion. The results of the present study suggest that IIR results in severe mucosal destruction within 6 h after reperfusion, associated with mast cell activation and substantial increases in the mast cell counts.