Background: Wampee (Clausena lansium (Lour.) Skeels) is an understudied Rutaceae crop native to southern China, whose fruit features a complex aroma profile with simultaneous sour, sweet, bitter and astringent notes. Although bioactive compounds including flavonoids, alkaloids and volatile oils in wampee fruit have been partially characterized, the tissue-specific metabolic and transcriptional basis underlying its distinctive aroma formation remains largely unclear. Methods: We performed an integrated volatile metabolomic and transcriptomic analysis on the pericarp (peel) and flesh of wampee fruit across three cultivars (Shanyellowpi, Heijingang, Bingtangxin). Volatile metabolites were profiled via headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS), and transcriptome profiles were generated by RNA-Seq. Multi-omics integration was conducted using Procrustes analysis, gene–metabolite correlation network construction and weighted gene co-expression network analysis (WGCNA). Results: A total of 288 volatile metabolites were identified, representing the most comprehensive volatile inventory for C. lansium reported to date. Principal component analysis and partial least squares discriminant analysis revealed distinct volatile profiles between pericarp and flesh; terpenoids were the dominant chemical class, accounting for 71.56–91.48% of total volatiles in pericarp and 61.88–67.22% in flesh. Notably, organoheterocyclic compounds were significantly enriched in Shanyellowpi flesh (40.45%), forming a cultivar-specific metabolic signature absent in the other two cultivars. Transcriptomic analysis showed that phenylpropanoid biosynthesis was the most significantly enriched pathway among differentially expressed genes, followed by monoterpene biosynthesis and sesquiterpenoid biosynthesis. Procrustes analysis demonstrated a strong global concordance between the two omics layers (M² = 0.535, p < 0.001). Gene–metabolite correlation networks identified terpene synthase (TPS) genes (HP075360, HP217350) and oxidoreductase genes (SOD1, GST, 10HGO) as candidate co-regulators of terpenoid biosynthesis. WGCNA further prioritized TPS genes, cytochrome P450 genes and MYB transcription factor genes as key regulators driving volatile metabolic divergence between tissues. Conclusion: This study provides a comprehensive volatile and transcriptomic atlas of wampee fruit, and identifies tissue-specific and cultivar-specific metabolic signatures as well as their candidate regulatory genes. These findings advance our understanding of quality differentiation in Rutaceae fruits and lay a foundation for molecular breeding and flavor improvement of wampee.