This paper has been tried to measure technical, allocative and economic efficiency of natural gas refineries of Iran during 2003-2009 with using nonparametric data envelopment analysis (DEA) and Malmquist index. For this purpose, the input based method with three inputs and two output is used. The results showed that the average technical, allocative and economic efficiency, of provinces of the country during 2003-2009, respectively is 95 percent, 98.1 percent and 93 percent. Among natural gas refineries for calculation of the productivity, two refinery, on average, have experienced during 2003-2009 positive growth, and 4 other refinery, have experienced negative growth in productivity. During the year, interest in total factor productivity refineries growers an average of 8.2 percent had negative growth, negative growth of 8 percent due to changes in Technology efficiency.