In order to study the influence of factor inputs and institutional innovation on grain production in different regions, this article takes agricultural data of Shandong Province, Jiangxi Province and Sichuan Province in 1978-2011 as samples, to analyze five factor inputs: land area, labor forces, fertilizer volume, mechanical power input and effective irrigational area. At the same time, the research compares the impact of the household contract responsibility system and rural tax reform policies on grain production in different regions. The three provinces represent eastern, central and western regions respectively. Different regional agricultural resources lead to the different influence of each factor input and system implementation. Land element can promote grain production in the central region, but it has no significant effect in eastern and western regions. Labor element can promote grain production in central and western regions, but it has no significant effect in eastern region. Fertilizer element has significant effect on grain production in all three regions. Mechanical power inputs can promote grain production in eastern region, but it has no effect in central and western regions. The irrigation area plays no significant role in grain production in three regions. The household contract responsibility system and rural tax reform policies have promoted grain production in three regions. Thus, different resource endowment in these three regions is leading to different influence on grain production. Promoting grain production should consider the factors of regional differences.