Employing sesame cake fertilizer increased oil content and quality of tobacco leaves. But the mechanism was still unknown. To investigate the mechanism, the genes expression profile of tobacco leaves was explored by cDNA microarray analysis when applying sesame cake fertilizer. There were 54 differently expressed genes (with log ratio values ≥1 or ≤-1) among 22810 genes set in a microarray plate, in which 32 genes up\|regulated and 22 down\| regulated compared with control. Functional analysis showed that the genes closely related with tobacco leaves quality were down\|regulated, such as dihydroflavonol 4\|reductase family genes, which responses to flavonoid synthesizion, and GTs, which accelerate glucide anabolism. While many genes, e.g. CslD3 (relation with fibrial growth), ATPase subunit 6 (driving transportation of ion and small molecule metabolic productions), and the genes that promote the synthesis of aminophenol, were up\|regulated. Furthermore, some genes that related to photosystem (psaK, PsbI, for example) and replication, transcription, translation and protein folding (such as SWIM zinc finger family protein, histone H4, mTERF\|related, etc), were differentially expressed. 19 unknown function genes also expressed differently. The results indicated that employing sesame cake fertilizer had an effect on the genes expression of tobacco leaves and could consequently improve the quality of tobacco leaves.