To investigate the effect of propofol on the expression of rabbit ischemia-reperfusion injury-related proteins and the mechanism involved. Thirty healthy adult New Zealand rabbit were selected. After establishment of liver I/R model, the rabbits were divided into group A (sham operation group), group B (control group using saline), and group C (propofol group) with ten rabbits in each group. The total protein concentration, differentially expressed protein spots and the difference of apoptotic proteins expression levels among the three groups were compared. The total protein concentrations in group A, B, and C were 0.778, 0.835, and 0.765 μg/μl, respectively, and the protein concentration in group B was significantly higher than group A and C (p < 0.05), with no significant difference between group A and C (p > 0.05); results analyzed by PDQuest software showed that the average number of protein spots and matching ratio had no significant difference among the three groups (p > 0.05); MALDI-TOF-MS mass spectrometry identified 16 differentially expressed protein spots; the numbers of Caspase-3 positive cells in group B and C were significantly higher than those in group A, and the numbers of Bcl-2 and Bax positive cells in group B and C were significantly lower than those in group A (p < 0.05); the number of Capase-3 positive cells in group C was significantly higher than those in group B, and the number of Bcl-2 positive cells in group C was significantly lower than those in group B (p < 0.05). The numbers of Bax positive cells had no significant difference between group B and C (p > 0.05); densities of Caspase-3, Bcl-2 and Bax in group B and C were significantly higher than those in group A (p < 0.05); Western blotting results from the comparison of the number of positive cells between group B and C was in accordance to the result obtained from immunohistochemistry. After I/R injury in rabbit, there was deregulation of various proteins such as Caspase-3, Bcl-2 and Bax, which was an important factor contributing to liver injury even systematic disease. Propofol could regulate the expression of I/R injury-related proteins and inhibit the attack of free radical to liver, having a remarkable advantage in preventing I/R injury and controlling the development of I/R injury. This study provides an effective theoretical basis for the prevention and treatment of I/R injury.