BackgroundThe disruption of seed dormancy is a complicated process and is controlled by various factors. Among these factors, membrane lipids and plant hormones are two of the most important ones.Paris polyphyllais an important Chinese herbaceous species, and the dormancy trait of its seed limits the cultivation of this herb.ResultsIn this study, we investigate the global metabolic and transcriptomic profiles ofParis polyphylladuring seed dormancy breaking. Widely targeted metabolomics revealed that lysophospholipids (lysoPLs) increased duringP. polyphyllaseed dormancy breaking. The expression ofphospholipase A2(PLA2), genes correlated to the production of lysoPLs, up-regulated significantly during this process. Abscisic acid (ABA) decreased dramatically during seed dormancy breaking ofP. polyphylla. Changes of different GAs varied duringP. polyphyllaseeds dormancy breaking, 13-OH GAs, such as GA53were not detected, and GA3decreased significantly, whereas 13-H GAs, such as GA15, GA24and GA4increased. The expression ofCYP707Aswas not synchronous with the change of ABA content, and the expression of mostUGTs,GA20oxandGA3oxup-regulated during seed dormancy breaking.ConclusionsThese results suggest that PLA2 mediated production of lysoPLs may correlate to the seed dormancy breaking ofP. polyphylla. The conversion of ABA to ABA-GE catalysed by UGTs may be the main cause of ABA degradation. Through inhibition the expression of genes related to the synthesis of 13-OH GAs and up-regulation genes related to the synthesis of 13-H GAs,P. polyphyllasynthesized more bioactive 13-H GA (GA4) to break its seed dormancy.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04262-3.