Previous studies have primarily focused on the effects of aggregate energy consumption, energy mix, and energy efficiency on green growth. However, empirical evidence on the effects of changes in the inter-industry energy consumption structure on green total factor productivity (GTFP) remains limited. Using industry-level data from Japan for 1995–2023, this study constructs a panel dataset and, drawing on the Green Solow Model as its theoretical framework, examines how changes in the inter-industry energy consumption structure affect GTFP. A two-way fixed effects model is employed, with additional analyses of industry heterogeneity and the structural and energy-use effects. The results show a significant negative relationship between changes in the inter-industry energy consumption structure and GTFP. The heterogeneity analysis indicates that this negative relationship is concentrated in the agriculture–forestry–services group, whereas it is not statistically significant in the manufacturing–transportation group. In the full sample, the structural effect is significantly and positively associated with GTFP, while the energy-use effect is not statistically significant. In the subgroup analysis, the energy-use effect is significantly negative in the agriculture–forestry–services group, whereas the structural effect is not statistically significant; neither effect is statistically significant in the manufacturing–transportation group. These findings indicate that the effects of energy consumption structure adjustment on GTFP vary across industries and that both the direction and the transmission channels of these effects depend on industry-specific patterns of energy use and production structure. Accordingly, rather than applying a uniform policy framework, differentiated adjustment strategies tailored to the characteristics of individual industries are warranted.