Using panel data of cities in JiangSu province ranging from 2004 to 2013, the article evaluates Green Total Factor Productivity (GTFP) based on unexpected output DEA-Malmquist index method, and then explores its changes. The GTFP differences between cities are quantitatively analysed by Green Regional Disparity Index (GRDI) method. The results show that, during the sample period, the GTFP in JiangSu fluctuates and reaches a peak in the short term, and the main reason of GTFP rising is the technological progress; GTFP is generally lower than the traditional Total Factor Productivity; according to the GRDI index, cities’ GTFP differences of dynamic evolution process can be divided into three stages. Finally, suggestions are given to realize the economic sustainable development and improve GTFP.