Cold stress limits the growth and productivity of Hevea brasiliensis, the primary source of natural rubber. This study investigated early transcriptomic responses in Reyan ‘7-33-97’ seedlings exposed to 4 °C, 10 °C, and 15 °C for 1, 2, and 4 h with room temperature (25 °C) as the control. RNA sequencing identified 9894 differentially expressed genes (DEGs), with the most significant transcriptional changes observed at 10 °C, indicating that genes to resist cold stress could not be mobilized at 4 °C, resulting in poor cold resistance of the rubber tree. KEGG enrichment analysis of DEGs between 10 °C (2 h) and 4 °C (2 h) revealed that genes involved in tryptophan metabolism (HbKynL.x1, HbKynL, HbCLP1, HbCLP2) and carbon metabolism (TCH4, XTH23), which contribute to cell wall modification, exhibited higher expression at 10 °C. Gene Ontology enrichment analysis highlighted significant involvement of “thylakoid,” “photosystems,” and “photosynthetic membrane,” alongside molecular functions such as “xyloglucan transferase activity” and “transcriptional regulator activity.” The interacting network of key pathways, including carbon metabolism (ko01200) and carbon fixation (ko00710) pathways, was sorted out, highlighting their integration with plant hormone signal transduction. Complex signaling networks, including MAPK, and kynurenine pathways coordinate the expression of cold-responsive genes and protective proteins, and it was confirmed and speculated that there is crosstalk response in cold defense mechanisms. Furthermore, 61 DEGs were associated with antioxidant processes, including major catalase and peroxidase enzymes. Our study shows that rubber trees physiological activities that respond to low-temperature signals cannot be carried out normally at 4 °C. The newly discovered metabolic pathway and the reason for abnormal cold signal transduction at low temperatures are the focus of future research on cold resistance.