Eucommia ulmoidesrubber particles (EuRPs) are organelles that synthesise and store E. ulmoidesrubber (EuR). In this study, the lipids dynamic change of EuRPs from leaf tissue at different growth period were investigated. The results showed that there were 1149 lipid species belonging to 39 lipid classes that were identified; TGs, DGs and Cers were the most abundant among all lipids of EuRPs. Lipid expression analysis demonstrated that the expression intensity of TGs was almost 1 × 104-fold and 10-fold higher than those of MGs and DGs, respectively. Among sphingolipids, the expression intensity of SoP, CerG2, GM3, SM and GerG3 increased throughout the duration of investigation (August–November 2021). Further analysis found that the Cers species accounted for 9.40% of total lipid species and the number of Cers species in EuRPs isolated from leaves in August was the most, with gradual decline in the following 3 months. Meanwhile, hierarchical clustering indicated that there were seven types of highly abundant lipid species in leaf EuRPs from September to November, i.e.SQDG (18:3/18:3), SQDG (34:3), SQDG (17:5/23:2), DGDG (38:12), Co (Q9), TG (16:0/16:0/18:3) and TG (39:1). Compared with leaf EuRPs in August, there were 79, 101 and 107 lipid species which showed significant differential expression in September, October and November. Based on the high expression intensity of SQDG in EuRPs, the correlation between the genes mediated in EuR or SQDG biosynthesis was further analysed, whereby the results indicated co-expression of some genes, which implies the synergistic regulatory role in SQDG EuR biosynthesis.