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<i>Zoysia japonica</i> is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of <i>Z. japonica</i> can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel <i>Z. japonica</i> biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular <i>Z. japonica</i> cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of <i>Phenylalanine ammonia-lyase</i> (<i>PAL</i>), <i>Homeobox-leucine Zipper IV</i> (<i>HD-ZIP</i>), and <i>ATP-Binding Cassette transporter B8</i> (<i>ABCB8</i>) expressions, as well as a unique down-regulation of <i>zinc-regulated transporters and iron-regulated transporter-like proteins</i> (<i>ZIPs</i>) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant <i>Z. japonica</i> variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.