Due to the extensive development model of "focusing on development with high investment" for a long time, the resources input of industry in Liaoning is seriously mismatched with economic output, resulting in serious waste of resources. In view of this, the consumption of virtual water and embodied energy was calculated through the input-output model, and they were incorporated into the undesired super-SBM to compare the virtual water efficiency, embodied energy efficiency and virtual water-embodied energy coupling efficiency of 23 sectors. Finally, we analyzed the dynamic change in coupling efficiency using the Malmquist index model. The results showed that: (1) Food and Tobacco was the largest consumer of virtual water, accounting for 31.3% of total consumption; Petroleum Product Processing was the largest consumer of embodied energy, accounting for 24.4% of total consumption. (2) Regarding the embodied resource transferring pattern, the total industrial transferrable flux decreased by 40.2% (virtual water) and 12.5% (embodied energy) from 2012 to 2018. Smelting and Pressing of Metals was not only an important supplier but also a significant recipient, receiving metal ore resources and transferring them to different equipment manufacturers. (3) On the whole, the embodied energy efficiency was greater than the virtual water efficiency, but neither had reached the production frontier in most sectors. The coupling efficiency of the overall industry showed a "V" trend, but the efficiency value did not reach 1. (4) Although total factor productivity (TFP) and the corresponding decomposition factors were significantly different in 23 sectors, pure technical efficiency (PEC) obviously restricted TFP in most sectors. In addition, scale efficiency (SEC) maintained a stable balanced, especially in heavy manufacturing industry. In contrast, technology efficiency (TC) severely constrained TFP especially in Chemical Products and Production and Supply of Water.