The efficient and coordinated development of industrialization, urbanization, informatization and agricultural modernization(so called “Sihua Tongbu” in China, and hereinafter referred to as “four modernizations”) is not only a practical need but also an important strategic direction of integrating urban-rural development and regional development in recent China. This paper evaluated the comprehensive, coupling and coordinated developmental indices of “four modernizations” of China’s 343 prefecture-level administrative units, and calculated their efficiency of “four modernizations” in 2001 and 2011. The efficiency evaluation index system was established. The efficiencies and their changing trend during the period 2001–2011 were investigated using the data envelopment analysis(DEA) model. Spatial-temporal pattern of the efficiency of China’s prefecture-level units was explored by using exploratory spatial data analysis(ESDA). Finally, the main influencing factors were revealed with the aid of geographically weighted regression(GWR) model. Results indicate that the comprehensive, coupling and coordinated developmental indices and efficiency of “four modernizations” of China’s prefecture-level administrative units have obvious spatial differences and show diverse regional patterns. Overall, the efficiency is relatively low, and only few units with small urban populations and economic scale are in DEA efficiencies. The efficiency changing trends were decreasing during 2001–2011, with a transfer of high efficiency areas from inland to eastern coastal areas. The difference between urban and rural per capita investment in fixed assets boasts the greatest influence on the efficiency. The efficient and coordinated development of industrialization, urbanization, informatization and agricultural modernization (so called “Sihua Tongbu” in China, and hereinafter referred to as “four modernizations”) is not only a practical need but also an important strategic direction of integrating urban-rural development and regional development in recent China. This paper evaluating the comprehensive, coupling and coordinated developmental indices of “four modernizations ” of China’s 343 prefecture-level administrative units, and calculated their efficiency of “four modernizations ”in 2001 and 2011. The efficiencies and their changing trend during the period 2001-2011 were investigated using the data envelopment analysis (DEA) model. Spatial-temporal pattern of the efficiency of China’s prefecture-level units was explored by using exploratory spatial data analysis (ESDA). Finally, the main influencing factors were revealed with the aid of geographically weighted regression (GWR) model. Results that that comprehensive, coupling and coordinated developmental indices and efficiency of “four modernizations ” of China’s prefecture-level administrative units have obvious spatial differences and show diverse regional patterns. Overall , the efficiency changing trends were decreasing during 2001-2011, with a few of units with small urban populations and economic scale are in DEA efficiencies. The efficiency changing trends were decreasing during 2001-2011, with a transfer of high efficiency areas from inland to eastern coastal areas. The difference between urban and rural per capita investment in fixed assets boasts the greatest influence on the efficiency.