Maize inbred line 08-641 was used as material to analyze the proteome difference during seed dormancy breaking by mean of 2-D electrophoresis method. The results showed that 600 protein spots were detected in fresh dormant seed and 620 protein spots were detected when seed dormancy was broken through 10d after-ripening, respectively. Among the 23 differential expressions Protein spots, there were 4 down-regulated protein spots, 4 up-regulated proteins, 8 protein spots with additional expression, and 7 protein spots with missing expression. The proteins identified by MALDI-TOF-MS were main involved in globulin, late embryogenesis abundant protein, legumin and other storage proteins; proteasome, sorbitol dehydrogenase which involved in metabolism; heat shock protein involved in protein structure and cell function regulation. The seed dormancy of maize inbred line 08-641 was due to lack of expression or over-expression of some dormancy-related proteins.