The Chinese government has grown increasingly invested in ecology in recent years. This paper discusses eco-efficiency using data envelopment analysis on 48 cities in Bohai Rim with special focus on the role of industrial structure upgrades. Based on the values from a super undesirable slack-based model, this study investigates eco-efficiency from temporal and spatial perspectives to reveal gaps among Bohai cities but an overall improvement in regional eco-efficiency. Moreover, this study adopts the Global and Local Moran's I to identify positive spatial autocorrelations and shows that most cites in Bohai Rim have high-high, low-low aggregation characteristics. Plus, the economic effects of per capita GDP, industrial structure upgrades on eco-efficiency are determined according to a spatial Durbin model. There appear to be negative spillover effects of industrial structure upgrades on surrounding cities, which reflects an industry transfer phenomenon related to eco-efficiency. Display omitted •Undesirable super slack based measure is exploited to measure eco-efficiency.•There is an increasing polarized regional disparity in eco-efficiency in Bohai Rim.•Local improvement can be obtained in eco-efficiency under the influence of industry structure upgrading.•As a consequence of industrial transfer, negative effects arise in eco-efficiency for the surrounding cities.