Acer truncatum Bunge exhibits remarkable cold tolerance at the mature seedling stage, yet the mechanisms governing its seed germination under low-temperature conditions remain poorly understood. To elucidate the molecular and physiological mechanisms underlying low-temperature germination in A. truncatum seeds, we selected A. truncatum seeds as the experimental material. The seeds were evenly divided into two groups and subjected to germination under 25 °C (control) and 4 °C (low-temperature stress) conditions, followed by transcriptome sequencing and physiological and biochemical analyses. Transcriptome sequencing analyzed differential genes and physiological indicators. Fourteen transcription factor families were identified (ARR-B, AP2-EREBP, bHLH, NAC, FAR1, MADS, WRKY, AB13VP1, bZIP, C3H, CROS, LOB, TCP, and SBP). These regulate seed germination under abiotic/biotic stress. GO term enrichment occurred in biological processes. KEGG enrichment involved carbon metabolism, the glutathione pathway, the citrate cycle, and glycolysis. Most genes were upregulated. Citrate cycle and glycolysis correlated with seed activity, promoting germination. The glutathione cycle greatly improves the stress resistance of seed germination. There were 1804 genes that were upregulated and 8075 genes that were downregulated during seed germination. Among differential genes, CBF 5 was significantly downregulated but most WRKY families and LEA14-A were upregulated to maintain cell homeostasis. Meanwhile, GSH, SOD, POD, and proline (Pro) levels increased with prolonged stress. MDA rose initially, then declined. Soluble protein content first increased, then decreased, but remained higher than controls. Seeds germinated under low temperature, but germination potential was slightly lower than at room temperature. We propose that LEA protein, antioxidant enzymes, and Pro accumulation enhance cold tolerance. This study elucidates the physiological and molecular mechanisms underlying seed germination, advancing the understanding of cold tolerance in A. truncatum.