Soil carbon pool, the largest carbon pool in any terrestrial ecosystems, has been disrupted owing to high rates of fertilization and intensive crop rotation. Reduction of soil carbon caused decreases of tobacco quality. Firstly, the correlations between soil types (purple soil and paddy soil from the tobacco region in southern China) and tobacco aroma compounds were analyzed in this research. It was showed that the soil carbon pool is closely correlated with tobacco aroma. Secondly, effect of the soil carbon content on soil microorganisms were analyzed. The results indicated that improvement of the soil carbon increased the tobacco aroma and the abundance of Lactobacillales and Oceanospirillales. The present study revealed the correlations between the soil carbon, microbial community structure and tobacco quality, demonstrating the importance of improving the soil carbon for increasing tobacco quality.