Effects of Carbonate Alkali stress on germination and seedling growth in Japonica rice were studied with two Japonica rice of Mianjing 147 and Hexi22-2. The results showed that when the concentrations of Carbonate Alkali below 20 mmol/L, the Carbonate Alkali stress has some facilitation to the germination and seedling growth of Japonica rice, and the chlorophyll contents of leaf was increased a little than that of control. But the degree of inhibition of the germination and the growth of leaf and root of Japonica rice was increased with increasing concentration of Carbonate Alkali. When the concentrations of Carbonate Alkali above 60 mmol/L, the chlorophyll contents of leaf was decreased rapidly, and the content of proline in leaf was rapidly increased. The results indicated that the tolerance concentrations of Carbonate Alkali was 60 mmol/L to germination and seedling growth of Japonica Rice.