'Allen Eureka' is a progeny variety of the variety ‘Eureka lemon’ due to bud mutation. This variety showed excellent performance at fruiting traits， while it was susceptible to winter defoliation， eventually resulting in severe leaf shedding and decreasing the yield production in the coming year. The mechanism of leaf shedding remains unknown. Two lemon cultivars （‘Allen Eureka’ and ‘Yunning No. 1’） with degrees of winter defoliation were used to investigate the molecular regulatory mechanisms of leaf abscission. The petiole abscission zones were collected at three stages， namely， the pre-defoliation stage （E24）， mid-defoliation stage （E48）， and post-defoliation stage （E72）， and subjected for transcriptome sequencing. The differentially expressed genes （DEGs） between two lemon varieties were identified， revealing a total of 14002466， and 935 DEGs in pre-defoliation stage， mid-defoliation stage， and post-defoliation stage， respectively. The largest number of DEGs was found in mid-defoliation stage. GO enrichment analysis revealed that these DEGs were mainly enriched in the processes of heme binding， tetrapyrrole binding， oxidoreductase activity， iron ion binding， transcription regulator activity and response to oxidative stress， cellular glucan metabolic process， glucan metabolic process， cell periphery， cell wall in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in mid-defoliation stage and involved in plant hormone signal transduction， phenylpropanoid biosynthesis， plant-pathogen interaction， and MAPK signaling pathway. By analyzing the genes with significant differential expression of the four pathways， 13 genes including xyloglucan endotransglucosylase/hydrolase protein， indoleacetic acid-induced protein， indole-3-acetic acid-amido synthetase， peroxidase， β-glucosidase， pathogenesis-related genes transcriptional activator AP2 and pathogenesis-related protein were selected.They might be associated with the regulation of lemon leaf abscission. qRT-PCR verified that the expression of these genes was consistent with the transcriptomic data. This study raised new insights in deciphering the lemon leaf abscission， as well as provided reliable data to identify lemon defoliation candidate genes and uncover the analysis of leaf shedding pathways.