Using DEA-Malmquist index method, we perform an empirical analysis of Japonica rice production input-output panel data in 12 China's major Japonica rice producing areas during 2001-2012, calculate the total factor input-output efficiency of China's major Japonica rice producing areas, and analyze TFP change and convergence of Japonica rice. It is found that from 2001 to 2012, the average growth rate of total factor productivity (TFP) was -2.3% and the technological progress was -2.2%, and the decline of technical progress was the main cause of the decrease of TFP. Moreover, significant differences exist between the TFP of these provinces, and the TFP of Heilongjiang and Jiangsu is higher than that of other provinces. Further convergence test indicates that TFP of the main producing areas shows σ convergence trend.