To study the stability of major latently fragrant substances of flue-cured tobacco of different varieties in Baoshan of Yunnan, three tobacco cultivars (K326, Y87 and Y99) in two soil types at three test sites with different altitudes were tested. The contents of major latently fragrant substances were measured and the effects of genotypes, environments and their interactions were analyzed by AMMI model. The results showed that genotypes, environments and their interactions had significant effects on the contents of lutein, β-carotene, and chlorogenic acid. The rutin content was mainly influenced by genotypes while the major latently fragrant substances and their stability were affected significantly by the interactions of genotypes and environments. The contents of lutein, β-carotene, and chlorogenic acid increased remarkably with altitude, and their stabilities were strengthened to different extents. K326 adapted well to middle-lower altitude, while Y87 and Y99 adapted well to middle-higher altitude.