Abstract: This work studied the effects of three storage methods on the quality, routine chemical components and surface bacterial diversity of flue-cured tobacco. The three methods were Method 1, mechanical dehumidification combined with phosphine fumigation; Method 2, mechanical dehumidification combined with sulfuryl fluoride fumigation; Method 3, controlled atmosphere storage. Samples of redried flue-cured tobacco were stored under the three storage methods for 24 months before routine chemical components and sensory quality of the samples were analyzed. In addition, surface bacterial diversity of the samples was investigated by nested PCR and denaturing gradient gel electrophoresis (DGGE). The results showed that:1) The sensory quality of tobacco from the same tobacco-planting areas stored with Method 1 was better than that with Method 2 or Method 3. The chemical indexes of tobacco from different tobacco-planting areas were different under the storage conditions. The tobacco stored with Method 3 had higher moisture contents and lower weight losses. 2) Tobacco leaves (C3F) from Shizong in Yunnan stored with Method 1 for 24 months had the highest surface bacterial diversity and diversity index, while those stored with Method 2 had the lowest diversity index. The amounts of surface bacteria stored with Method 3 were significantly different, which indicated that the distribution of bacteria on the surface of tobacco leaves was not even.