Using grain production panel data in 30 provinces in China from 2001 to 2010, this paper adopts a DEA-based Malmquist productivity index method to measure and decompose grain TFP (Total Factor Productivity) growth index of the nation’s main grain production areas, main grain sales areas, and balancing areas. This paper also analyzes the spatial and temporal disparities and the underlying mechanism of dynamic TFP index. On this basis, it continues to explore TFP and its decomposition value - exogenous influencing factor of technical efficiency index and technical progress index. Our results show that the TFP index of main production areas have realized an average annual increase of 0.28% within 10 years, which has benefited from technical improvement and efficiency enhancement. However, main sales areas have suffered from a duel loss in the technical progress and technical efficiency. As a result, TFP has an average annual decrease of 0.35%. TFP in balancing areas also has an average decrease of 0.69%, influenced by deterioration of technical progress. We also find that the implementation of the central government’s favorable policies to farmers has significant influence on improving grain TFP level in main production areas. However, these policies have a lagging influence on main sales areas and balancing areas. In addition, per capital grain production scale and mechanization level have negative influence on TFP growth in main grain production area, but positive influence on TFP in main grain sales areas. As for the grain production-sales balancing areas, expansion of the per capita production scale can improve the technical efficiency, but has a reverse inhibiting impact on TFP and technical progress. Finally, based on the research results, this paper proposes measures and suggestions to improve grain productivity more effectively.