Taraxacum kok-saghyz (TKS) has been investigated as an alternative rubber crop due to its comparability in rubber quality to the Para rubber tree, Hevea brasiliensis. However, the yield of natural rubber from TKS is relatively low, necessitating the development of effective strategies to enhance its production. In this study, we report that the rubber production of TKS was increased by about 40% through foliar application of a natural lipid, lyso-PE. To better understand the effect of lyso-PE on the biosynthesis of natural rubber, we performed transcriptome analysis in TKS latex. We identified 1258 differentially expressed genes in TKS latex after lyso-PE treatment, and through multiple analyses, we found that lyso-PE mediates genetic modulations in various metabolic pathways related to resistance response and secondary metabolite metabolisms. Among the natural rubber biosynthesis pathways, the mevalonate pathway leading to the production of a monomer (isopentenyl pyrophosphate) and the biosynthesis pathway of the initiators (geranyl pyrophosphate and farnesyl pyrophosphate) of rubber polymerization, as well as the expression of SRPP genes, were stimulated by lyso-PE treatment. This study with TKS root latex provides a novel and relatively straightforward method to enhance the yield of natural rubber through the exogenous application of a natural lipid, as well as fundamental knowledge for future research on improving natural rubber biosynthesis in TKS.