Papaya is a tropical fruit crop renowned for its rich nutrition, particularly pro-vitamin A. Aroma substances are a major component of fruit quality. While extensive research has been conducted on papaya aroma, there has been a notable lack of in-depth research into a specific class of substances. To bridge this gap, our study focused on analyzing the aroma components of various papaya varieties and their biosynthesis pathways. We compared the volatile components of three papaya varieties with distinct flavors at various ripeness stages. A continuous accumulation of linalool, a volatile compound, in the 'AU9' fruit was detected as it matured. The linalool content reached 56% of the total volatile components upon full ripening. Notably, this percentage was significantly higher than that observed in the other two varieties, 'ZhongBai' and 'Malaysian 7', indicating that linalool serves as the primary component influencing the papaya's odor. Subsequently, we identified CpTPS18, a gene associated with linalool biosynthesis, and demonstrated its ability to catalyze linalool production from GPP and enhance its accumulation through overexpression in papaya fruits, both in vivo and in vitro. Based on transcriptomic analysis, it was predicted that CpMYB56 and CpNAC56 may transcriptionally activate the expression of CpTPS18. Subsequent yeast one-hybrid assay and dual luciferase analysis revealed that CpNAC56 activates the transcription of CpTPS18. Transient overexpression in vivo demonstrated that this gene could upregulate the expression of CpTPS18 and promote linalool accumulation. These results uncovered the primary volatile molecule responsible for papaya fruit odor and identified two major genes influencing its biosynthesis. The genomic resources and information obtained from this study will expedite papaya improvement for fruit quality.