To investigate the floral aroma metabolism pathways and differentially expressed genes （DEGs） involved in the biosynthesis of terpenoid aroma compounds in tropical waterlily organs， the transcriptome sequencing was used to analyze the flower organs including the petal （PE）， stamen （ST） and pistil （PI） of N. ‘Paul Stetson’. The number of differentially expressed genes in PE-vs-PI， ST-vs-PI， and ST-vs-PE were 7853， 7501， and 2526， respectively. GO classification and enrichment analysis showed that these DEGs were mainly involved in biological regulation， cellular processes， metabolic processes， and stimulus response biological processes. KEGG annotation revealed abundant pathways with significantly enriched DEGs in PE-vs-PI， followed by ST-vs-PI， and ST-vs-PE. Ninety-eight of 794 DEGs that shared in three comparative groups were enriched in four terpenoid floral aroma synthesis pathways， and 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. Six of 98 DEGs were randomly selected and subjected for qRT-PCR analysis， confirming the trend on transcriptional expression as revealed by transcriptome sequencing. The results provided a scientific reference for future deciphering the molecular mechanism of terpenoid aroma compounds biosynthesis in tropical waterlilies.