The relationship between industrial structure (IS) and eco-efficiency (EE) is intricate with mutual influence and constraint. Exploring the coordinated relationship between IS and EE is beneficial to the sustainable development of ecologically fragile areas. This paper estimates and analyses the levels of EE and IS in 39 prefecture-level cities of the Loess Plateau, discussing the comprehensive and coordinated development levels between industrial structure rationalization (ISR) and EE, industrial structure advancement (ISA) and EE based on the coupling coordination degree model (CCDM). The results showed that the comprehensive development of the Loess Plateau has rough and imbalanced issues. The EE and IS are developing at a relatively low level, and the spatial distribution shows the development trend of high in the east and down in the west. The CCD of ISA and EE performs better than that of ISR and EE, but neither has reached the collaborative coupling state. The poor CCD score in the Loess Plateau is primarily attributable to its relatively backward degree of integrated EE and IS. The results are expected to provide decision-making support for EE improvement and industrial restructuring in the Loess Plateau and other ecologically fragile areas.