Abstract: 【Objective】 The cornicle of aphids is an important organ for secreting defensive chemicals. Cornicle transcriptome sequencing and analysis can provide molecular basis for identification of genes related to aphid alarm pheromone synthesis and release. 【Methods】 Transcriptome sequencing and comparative analysis were performed on the cornicles and residues of Megoura crassicauda using Illumina NoveSeq 6000 sequencing platform. The candidate genes were identified in the synthesis and release of alarm pheromones using analysis of the differentially expressed genes (DEGs), and the expression patterns of these genes were further verified by real-time Quantitative PCR (RT-qPCR). 【Results】 A total of 2156 genes were identified as DEGs between the cornicles and the residues (expression difference ≥2 times). Cytochrome P450 monooxygenase (CYP450) and terpene synthase (TPS) gene families, which might be involved in terpene synthesis alarm pheromone synthesis, were analyzed. Among them, the expression levels of three CYP450s (McraCYP380C, McraCYP4CK1 and McraCYP315A1) in the cornicles were significantly higher than those in the residues. Two isoprenyl diphosphate synthase (IDS) genes, namely farnesyl pyrophosphate synthase (FPPS) and geranyl pyrophosphate synthase (GPPS), were identified. There were no significant differences in the expression levels of FPPS and GPPS between tissues. In addition, potential genes related to alarm pheromone release and transport were analyzed, and two chemosensory protein (CSP) genes were identified as being highly expressed in the cornicle. The expression levels of McraCYP380C, McraCYP4CK1, McraCYP315A1 and McraCSP7 genes in the cornicle were significantly up-regulated. 【Conclusion】 The DEGs in the cornicles and the residue transcriptome of M. crassicauda are successfully identified and analyzed.