China’s carbon emissions have a stable industrial concentration. In recent years, the carbon emissions of the six major high-carbon industries have accounted for approximately 80% of the national total and are thus priority areas for emission reduction. With the promotion of energy-saving and emission-reduction policies, the structure and scale of high-carbon industries in various regions have undergone changes, but their carbon reduction effects show significant regional differences. Based on China’s provincial panel data from 2006 to 2020, this study discusses the structural characteristics of high-carbon industries with their proportion of energy-based industries and measures their scale characteristics with their output values. On this basis, a fixed-effects model is used to analyze the single and synergistic effects of the scale and structure of high-carbon industries on carbon emissions in each province. The results indicate that changes in the scale and structure of high-carbon industries significantly affect carbon emissions but show regional differences in both the single and synergistic effects. When considering these synergistic effects, the single effect of high-carbon industries on carbon emissions will be weakened. In regions with large-scale high-carbon industries, the increase in the proportion of energy-based industries significantly increases carbon emissions, but this effect gradually weakens as the overall scale expands. In areas with small-scale high-carbon industries, the increase in the proportion of energy-based industries has a relatively small effect on carbon emission growth that gradually increases with the overall scale. In addition, the implementation of the carbon emission trading policy has a significant moderating effect on the carbon emissions of high-carbon industries and strongly promotes its reduction.