To investigate the relationship between soil organic matter content and flue-cured tobacco quality, 222 pairs of soil and tobacco leaves samples were collected from typical tobacco fields in Wenshan, Yunnan Province, the contents of soil organic matter (SOM, 0–20 cm) and the appearance qualities, physical indicators, conventional chemical components and sensory qualities of tobacco leaves were determined and calculated, and the correlation between SOM content with the quality indicators of tobacco leaves were analyzed, and the quality indicators of tobacco leaves under different SOM content grades were compared. The results showed that: 1) In terms of appearance quality of tobacco leaves, SOM content was positively correlated to body score (P < 0.05), and significantly negatively correlated with color intensity score (P < 0.05). The color score under SOM grade Ⅱ (10–20 g/kg) was the highest and significantly greater than SOM grade Ⅳ (30–40 g/kg). 2) In terms of physical indicators of tobacco leaves, SOM content reached a significantly positive correlation with filling value score (P < 0.01), significantly negative correlation with stem content score (P < 0.05) and equilibrium moisture content (P < 0.01). The stem content score under SOM grade Ⅰ (≤10 g/kg) was higher and significantly greater than SOM grade Ⅴ (> 40 g/kg). 3) In terms of conventional chemical components of tobacco leaves, SOM content was significantly positively correlated with reducing sugar and total sugar ratio (P < 0.05), significantly negatively correlated with sugar-base ratio (P < 0.05) and total sugar content (P < 0.01). 4) In terms of sensory qualities of tobacco leaves, SOM content showed a significant negative correlation with the scores of fineness and softness and aftertaste (P < 0.05), and a highly significant negative correlation with the scores of roundness and total smoking evaluation (P < 0.01). The fineness and softness score under SOM grade Ⅰ was the highest and significantly higher than SOM grade Ⅳ (P < 0.01). The roundness score under SOM grade Ⅰ was the highest and significantly higher than SOM grade Ⅲ (20–30 g/kg), Ⅳ and Ⅴ (P < 0.05). The comprehensive analysis indicated that with the increase of SOM content, most indexes of tobacco leaf quality increased at first and then decreased, the quality of tobacco leaves was better under SOM grade Ⅱ-Ⅲ in the research area, which suggested the amount of organic fertilizers should be adjusted according to SOM content properly.