The discrepancy analysis of more than 700 flue-cured tobacco germplasm resources has been researched in the aspects of botanical traits, primary characters, disease resistant and tobacco leaf chemical component. The results showed that the discrepancy of flue-cured tobacco germplasm resources were mainly in the plant type, leaf shape, leaf auricle, leaf apex, angle of leaf and inflorescence. In addition, the main characters had certain differences. The range of plant height, wiping plant height, total leaves, node distance, stem, breadth and length of middle leaf were 97.0-326.0cm, 75.3-133.7cm, 8.6-54 leaves, 2. 6-10. lcm, 6.3-13.8cm, 41.6- 99.0cm, 16.6-47.8cm respectively. The range of proportion of the lower leaf, cutters, and upper leaf are 1.3- 3.7,1.5-4.9,1.6-5.8 separately. The range of budding period stage was 30-100 days. The coefficients of variation of the main characters were 7.8%-30. 3%. There were great differences in tobacco leaf chemical component for different germplasm resources, and the coefficient of variation was from 16.4% to 69.2%. Among 702 germplasm resources, the percentage of disease resistance, medium resistance, susceptibility, medium susceptibility was 18.2% , 36.0% , 6.6% , 39.0% respectively, and the considerable germplasm resources may offer the breeders with multiple choices in the future breeding programs.