Camellia oleifera is an important woody edible and industrial oil tree species. However, its fruits quality and production are severely affected by low temperature during flowering. In a previous study, we observed significant amounts of a honey-like mucilaginous substance at the base of C . oleifera flowers during cold acclimation, which could reduce flowers and fruits drop. However, the transcriptional regulation mechanism of C. oleifera in response to low-temperature stress remains unknown. In this study, we conducted targeted metabonomic and transcriptomic analyses using ultra-performance liquid chromatography–tandem mass spectrometry and next-generation sequencing technology. It was found that sugar content ( D -fructose, inositol, glucose, and sucrose) was increased as low-temperature stress conditions persisted over time. Besides, auxin was induced at the early stage of low-temperature stress, and long-term low-temperature stress induced the accumulation of abscisic acid and salicylic acid. Transcript-level changes in C . oleifera flower buds were related to the duration of low-temperature stress. A total of 381,812 unigenes were generated through transcriptome analysis, and several low-temperature -stress-induced differentially expressed genes (DEGs) were found to be involved in sugar accumulation and metabolism, including genes encoding sucrose phosphate synthase, sucrose synthase, invertase, UDP glucose pyrophosphorylase, trehalose-6-phosphate synthase, trehalose-6-phosphate phosphatase, galactinol synthase, raffinose synthase, sucrose transporters, sugars will eventually be exported transporters (SWEETs), and hexokinase. We also identified a large number of protein-kinase and hormone-related genes involved in signal transduction such as Aux/IAA , SAUR , GH3 , GST , PP2C , SnRK2 , MAPK , RLK , CDPK , and CIPK . Weighted gene co-expression network analysis indicated that the transcription factor WRKY may participate in the low-temperature-stress response of C. oleifera flower buds by regulating key genes involved in sugar metabolism. The self-protection mechanism of C. oleifera buds under low-temperature stress at the flowering stage is a significant discovery that will contribute to the identification of low-temperature stress tolerance-related genes for future breeding programmes. • Camellia oleifera is an important woody oil and industrial tree species, but it often encounters cold weather during the flowering period, resulting in low fruit set rates and yield declines. However, there are few studies on the molecular mechanism of its cold resistance. • We observed an interesting phenomenon that large amounts of a honey-like mucilaginous substance were induced at the flower base, and this study is to explore transcriptional regulation mechanism underlying the formation of this honey-like mucilaginous substance. • In this study, we identified key cold-related genes involved in signal transduction and glycometabolism, and for the first time indicated that WRKY may participate in the C. oleifera flower bud cold-stress response by regulating key genes involved in sugar accumulation and metabolism.