The synergistic advancement of industrial upgrading and energy eco-efficiency is crucial for the attainment of the Sustainable Development Goals. This study explored the coupling coordination relationship and its spatial-temporal evolution characteristics between industrial structure advancement and energy eco-efficiency, industrial structure rationalization and energy eco-efficiency in Yellow River Basin cities from 2010 to 2020. The super-SBM model and coupling coordination degree model were used to calculate the energy eco-efficiency and coupling coordination degree. Moran's I and Tobit model were used to analyze the spatial autocorrelation and the factors of coupling coordination degree. The coupling coordination degree of industrial structure advancement and energy eco-efficiency decreased from 0.535 to 0.489, with a growth rate of −8.60 %, showing a fluctuating downward trend. The coupling coordination degree of industrial structure rationalization and energy eco-efficiency decreased from 0.296 to 0.246, with a growth rate of −16.88 %, showing an "M" -shaped downward trend. The coupling coordination degree had a significant spatial correlation, and the global Moran's I value was stable around 0.2. Additionally, public transport and degree of opening-up can significantly promote the coordination relationship between industrial upgrading and energy eco-efficiency. These consequences can supply evidence for industrial and energy structure adjustment in river basin cities.