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<i>Camellia japonica</i> (Naidong), a rare temperate arbor in the genus <i>Camellia</i>, is an ornamental plant with high economic value. To understand transcriptional changes of the drought response in <i>C. japonica</i>, a comparative transcriptome analysis of <i>C. japonica</i> (Naidong) was conducted at two drought stages (0 and 20 DAF) based on the PacBio platform. The results showed significant differences in 265 genes and 3383 lncRNAs. Of these, 150 were upregulated and 115 were downregulated. Functional analysis revealed the involvement of distinct genes in 43 pathways. The biosynthesis of amino acids and the circadian rhythm of the plant were significantly enriched, with a significant change in <i>CjGST</i> potentially playing an important role under drought stress. In addition, three differential protein interaction network modules composed of 45 differentially expressed genes were predicted, which involved E3 ubiquitin ligases and threonine synthetic proteins. Moreover, a transient expression experiment demonstrated that overexpression of <i>CjGST1</i> in camellia leaves significantly increased leaf area compared to wild variants under drought stress, resulting in higher drought resistance. These findings provide a valuable resource for studying the genus <i>Camellia</i> while shedding new light on the molecular mechanisms of drought stress.