Citron (Citrus medica L.) peel essential oil is rich in terpenoids, but their composition and formation mechanisms remain unclear. We analyzed volatile compounds and gene expression in citron peel across three developmental stages using GC-MS and RNA-seq. GC-MS identified 91 volatiles, with γ-Terpinene and D-Limonene the most abundant; terpenes dominated (95.60–87.72%) but decreased with maturation, with 19 differential terpenoid metabolites. Differential expression analysis identified 10,238 genes with significant changes across three stages, including 256 TPS genes and 656 transcription factors. Via WGCNA and correlation analysis, 10 gene–metabolite pairs were identified, including 5 key genes and 2 transcription factors linked to nerol synthesis. These findings provide a framework for future research on citron genetics, terpenoid identification, and regulatory mechanisms of terpenoid biosynthesis.