Improving the industrial eco-efficiency of Yangtze River economic belt is an important road to promote industrial transformation, upgrading and green development; additionally, it is indispensable to push forward the coordinated development of regional economy and ecology. We divided industrial ecosystem into three subsystems that is economy, environment and energy. Then, based on industrial data of 9 provinces and 2 municipalities in 2009-2013, we adopt network DEA model to evaluate the industrial eco-efficiency and its corresponding subsystems. Results show that:(1) Industrial eco-efficiency in the Yangtze River economic belt is on the rise and also it is increasing from upstream to downstream. (2) For the economic subsystem, its industrial eco-efficiency is relatively stable and it is highest in the downstream area, lowest in the upstream area. Regarding the environmental subsystem, its industrial eco-efficiency continues to grow and it is highest in the downstream area, lowest in the midstream area. With respect to the energy subsystem, its industrial eco-efficiency is also increasing and it is highest in the downstream area, lowest in the upstream area. (3) The convergence test shows the industrial eco-efficiencies of provincial ecosystem and its subsystems have a convergent tendency where the economic subsystem is in the relatively stable condition. Lastly, we provide practical insights into policies for improving the industrial eco-efficiency of Yangtze River economic belt.