Field experiment was done to investigate the effects of different fertilizations (no fertilization, chemical fertilizer, organic-inorganic compound fertilizer, manure and chemical fertilizer) on organic acid in flue-cured tobacco from Baoshan, Yunnang. The results showed that 3 different fertilization treatments could increase the content of volatile acid, non-volatile acid and higher fatty acid in flue-cured tobacco. Compared with the chemical fertilizer treatment, the treatments of organic-inorganic compound fertilizer and manure and chemical fertilizer can more effectively improve the content of main non-volatile acid (malic acid and citric acid), higher fatty acid and the most of volatile acids except isobutyric acid and nonanoic acid in flue-cured tobacco, which enhance the quality of tobacco leaves. The influence of organic-inorganic compound fertilizer and manure and chemical fertilizer on the content of volatile acid in flue-cured tobacco was not notable; but organic-inorganic compound fertilizer treatment was more effective to improve the non-volatile acids and higher fatty acids in tobacco.