Rheum pumilum
stands as both a quintessential alpine plant and a significant traditional Chinese and Tibetan medicinal herb. Unraveling the molecular intricacies of seed germination in
Rh. pumilum
not only unveils the genetic foundations of plant seed germination strategies in high-altitude environments but also offers insights for cultivating
Rh. pumilum
medicinal materials. Employing transcriptome sequencing and the Weighted Gene Co-expression Network Analysis, this study delved into the shifts in gene expression levels across various stages of seed germination in
Rh. pumilum
. The process of seed germination in
Rh. pumilum
entails a cascade of complex physiological events. Six hormones (ABA, IAA, ETH, GA, BR, CK) emerged as pivotal players in seeds breaking in shells and the facilitation of rapid seed germination in
Rh. pumilum
. Fourteen transcription factor families (LOB, GRAS, B3, bHLH, bZIP, EIL, MYB, MYB related, NAC, TCP, WRKY, HSF, PLATZ, and SBP) along with four key genes (E2.4.1.13, EIN3, BZR, and BIN2) were identified that may be associated with both biotic and abiotic environmental stress. The ETR, ACACA and ATPeV0C genes were linked with energy accumulation during the initial stages of seed germination, CYP707A may play an important role in breaking seed dormancy, while the BRI1 gene may be correlated with swift seed germination. Additionally, several unidentified genes were recognized to play key roles in seed germination of
Rh. pumilum
, warranting further investigation. Moreover,
Rh. pumilum
demonstrates full activation of crucial physiological functions such as energy metabolism, signal transduction, and responses to biological and abiotic stresses during the seed breaking in shells. This study provides molecular evidence elucidating the swift seed germination strategies adopted by alpine plants to thrive in high-altitude environments. Furthermore, it serves as a foundational reference for enhancing seed germination rates and breeding practices to promote the sustainable development of
Rh. pumilum
medicinal materials.