Urban ecological civilization depends upon ecological efficiency. This paper, based on the panel data from 2005 to 2016 of 107 cities in Yangtze River economic zone, uses SBM to measure their ecological efficiencies and to discuss their temporal-spatial evolution rules of ecological efficiency by means of exploring spatial analysis and spatial Markov Chain, and studies the impacts of their driving forces. The study shows a general stable ecological efficiency as an upward staged distribution among up-, middle- and down-stream with partial areas showing polarization. There is a spatially connected effect in ecological efficiency development among cities. Cities of high ecological efficiencies promote their neighboring cities by positively overflowing, and cities of low ecological efficiencies pull down their neighboring cities. Population scale and industrial upgrade play a different role in different streams, promoting ecological efficiency of the down-stream but suppressing that of the middle- and up-stream. U-shaped connection between industrial upgrade and ecological efficiency implies that ecological efficiency may not be improved during industrial upgrade in a short term. Economic growth boosts a higher ecological efficiency.