The Yangtze River Economic Zone is a model zone for regional development strategy and a model zone for ecological culture construction as well. This paper, based on 107 cities along the zone, uses the shift-share to analyze its industrial transfer trend and finds that the transfer mainly out of down-stream goes to the up-stream with core to non-core cities at an interactive transferring. This paper establishes a 2003-2016 panel data model which verifies that pollution comes with this transfer, varying at time and space. Industries with discharge as waste water and dusts are transferred, but ones with discharge as sulfide dioxide are not. After 2011 the environmental policies get tighten, effectively decreasing the discharge of waste gas and water, but increasing the dusts. Policies are suggested in accordance with local environment and industries, offering references for transferring orderly industries in the Yangtze River Economic Zone.