In order to study if ecological efficiency is improved by industrial upgrading in the Yangtze river economic zone, this paper uses the ultra-efficient DEA model to measure ecological efficiency, applies new EKC to ecological efficiency, and employs spatial accounting model to testify if there is an EKC relation between industrial upgrading and ecological efficiency in thirty three cities in the Yangtze river economic zone. The results show a rising ecological efficiency, which is higher in the upper reaches than in the middle-lower reaches. A U-shaped relation exists between industrial upgrading and ecological efficiency, with most cities locating on the right of U shape, just over the turning point. Economic development has no significant effect on ecological efficiency, but environmental controls and foreign direct investment do. This paper suggests an interaction in ecologically environmental protection between the upper- and lower- reaches, industrial upgrading that can promote ecological efficiency in the upper-middle reaches, boosting environmental controls and rationally using foreign capitals.