Objective To probe the change of the structure and function of the small bowel by injection of different drugs (verapamil, energy compounds or normal saline) via the superior mesenteric artery (SMA) injections.Methods The model of the small intestine ischemia/reperfusion (I/R) injury was made in grey rabbits. Free calcium concentration in mitochondria of the small intestine was determined, and the ultrastructural change was also observed by electron microscopy at the very time of occlusion, 60 minutes after occlusion and 30 minutes after reperfusion. Results The free calcium concentration in mitochondria was more declined in verapamil group (2.976±0.410 nmol/mg.prot) than in N.S. group (4.234±0.542 nmol/mg.prot), Ｐ＜0.01, at 60 minutes after occlusion. At 30 minutes after reperfusion, free calcium concentration in mitochondria was more decreased in energy compunds group (2.401±0.323 nmol/mg.prot) and verapamil group (3.847±0.610 nmol/mg.prot) than in the N.S. group (5.981±1.031 nmol/mg.prot). Conclusion Verapamil and energy compouds have protective effects on the functions and ultrastructures of the I/R of small intestine.