The plant embryo is the germination center of the seed. How an embryo forms during seed maturation remains unclear, especially in the case of monocotyledonous plants. Generally, the complex processes of embryogenesis result from the action of a coordinated network of genes. Thus, a large-scale survey of changes in protein abundance during embryogenesis is an effective approach to study the molecular events of embryogenesis. In this study, two-dimensional gel electrophoresis (2DE) was applied to separate rice embryo proteins collected during the three phases of embryogenesis: 6 days after pollination (DAP), 12 DAP, and 18 DAP. We then employed matrix-assisted laser desorption-ionization time of flight/time of flight mass spectrometry(MALDI TOF/TOF MS) to identify the phase-dependent differential 2DE spots. A total of 66 spots were discovered to be regulated during embryogenesis, and of these spots, 53 spots were identified. These proteins were further categorized into several functional classes, including storage, embryo development, stress response, glycolysis, and protein metabolism. Intriguingly, the major differential spots originated from three globulins. We further examined the possible mechanism underlying the globulins multiple forms using Western blotting, proteolysis, and blue native gel electrophoresis techniques and found that the multiple forms of globulins were produced as a result of enhanced proteolysis during embryogenesis, indicating that these globulin forms may serve as chaperone proteins participating in the formation of multiple protein complexes during embryogenesis.