Grey mold is a common disease in tomato production caused by Botrytis cinerea, a necrotrophic pathogen, which often leads to dramatic reduction of tomato yield. Sucrose catabolism plays an important role in plant defense against pathogen infection by providing carbon skeleton and energy for plant defense responses and/or regulating the expression of defense-related genes through signaling pathway. Previous studies have shown that cell wall invertase (CWIN), a kind of sucrose-degrading enzyme, can enhance plant resistance to several necrotrophic pathogens. However, no research has been conducted to study the role of CWIN in tomato resistance to B. cinerea. In this study, wild type tomato (W) and its transgenic line (R) with elevated CWIN activity were used as materials to study the effect of CWIN on tomato resistance to B. cinerea (Bc) via in vitro inoculation. In addition, inoculated leaves were sampled 12 h and 60 h post inoculation (hpi) for RNA-Seq to elucidate possible molecular mechanisms underlying the regulation of CWIN to tomato resistance against B. cinerea. The results are as follows: (1) Elevated CWIN activity enhanced tomato resistance to B. cinerea; (2) KEGG annotation showed that DEGs (W-Bc-12 h-vs-R-Bc-12 h) from 12 hpi were significantly enriched in five pathways, including biosynthesis of secondary metabolites, metabolic pathways, DNA replication, starch and sucrose metabolism, and steroid biosynthesis; No significant enrichment pathway was found for DEGs (W-Bc-60 h-vs-R-Bc-60 h) from 60 hpi. (3) By mapping DEGs to plant-pathogen interaction pathway, it was revealed that the LRR-receptor serine/threonine-like kinase gene FLS2 and heat shock protein gene HSP90 involved in hypersensitive response and defense-related gene induction were up-regulated in RNAi leaves after inoculation, indicating the two genes may participate in the regulation of CWIN to tomato resistance to B. cinerea. (4) The analysis of plant hormone signal transduction pathways and MapMan mapping showed that the signal pathway of jasmonic acid (JA) and ethylene (ET) was enhanced in RNAi leaves after inoculation, while the signal pathway of salicylic acid (SA) was weakened, indicating that the hormones might work together to improve the resistance of RNAi tomato to B. cinerea. In addition, the signal transduction of growth-promoting hormone auxin (IAA) and cytokinin (CTK) was also enhanced in RNAi leaves after inoculation, but that of senescence-promoting hormone abscisic acid (ABA) was weakened. The changes in signal pathways of IAA, CTK and ABA could inhibit the cell death in host during bacterial infection, thus preventing the necrotrophic pathogen B. cinerea from obtaining necessary nutrients from the dead host cells for its infection. In addition, MapMan mapping also revealed that cell wall thickening, proteolysis, reactive oxygen species (redox state and peroxidases) and secondary metabolites were also greatly enhanced in RNAi leaves after inoculation, which all contribute to improving the disease resistance of tomato. In conclusion, this study showed that elevated CWIN activity enhanced tomato resistance to B. cinerea. Transcriptome analysis not only verified the existing molecular mechanisms underlying the regulation of CWIN to plant resistance to microbial pathogens, such as cell wall thickening, accumulation of reactive oxygen species (ROS) and hypersensitive response (HR), accumulation of resistance hormones (SA and JA/ET), biosynthesis of pathogenesis-related protein (e.g. PR and HSP proteins) and secondary metabolites (such as phytotoxins and phenolics), but also revealed several possible new mechanisms including the signal transduction of growth-promoting hormone (IAA and CTK) and senescence-promoting hormone (ABA) and proteolysis. This study can provide theoretical guidance for the improvement of tomato resistance to B. cinerea by using modern biotechnologies such as genetic engineering and molecular breeding.