To investigate the floral aroma metabolism pathways and differentially expressed genes involved in the biosynthesis of terpenoid aroma compounds in different parts of tropical waterlily organs. The transcriptome sequencing technique was used to analyze the petal (PE), stamen (ST) and pistil (PI) of the flower organ of N. ‘Paul Stetson’. According to the results, the Clean Data obtained from the three sites were greater than 6.30Gb, all of the Q30 base percentage was higher than 90.09% , and the GC-content was 48.42~50.31%. The analysis results of DEGs in three site samples showed that the number of differentially expressed genes in PE vs PI, ST vs PI, and ST vs PE was 7853, 7501, and 2526, respectively. The number of DEGs in the first two groups was similar. GO classification and enrichment analysis showed that the DEGs of the three comparative groups were mainly involved in biological regulation, cellular processes, metabolic processes, and stimulus response biological processes; KEGG classification and enrichment analysis showed that the KEGG pathway with significantly enriched DEGs in PE vs PI was the most abundant, followed by ST vs PI, with ST vs PE being the least. 98 DEGs involved in the terpenoid metabolism were selected from 794 DEGs in three comparative groups, which were enriched in four terpenoid floral aroma synthesis pathways, and the number of DEGs in PE vs PI and ST vs PI was higher than that in ST vs PE. In petals and stamens, the genes responsible for synthesis of acacia aldehyde and diterpenoid kaurene, were expressed at higher levels than in pistils. A total of six genes were randomly selected from 98 DEGs for qRT-PCR verification, and ttranscriptome sequencing confirmed the trend of gene expression. The results provide a scientific reference for the molecular mechanism of terpenoid aroma compounds biosynthesis in tropical waterlilies.